comp-chem/NWChem
1
0
Fork 0
mirror of https://github.com/nwchemgit/nwchem.git synced 2026-07-21 06:25:21 -04:00
Code Issues Projects Releases Packages Wiki Activity Actions 4

HTML files describing nwargos

Browse source
This commit is contained in:
Tjerk Straatsma 1996-06-26 23:05:32 +00:00
parent 0fda2b8bbd
commit 7237796f11
33 changed files with 2529 additions and 0 deletions
Download patch file Download diff file Expand all files Collapse all files

9
doc/nwahtml/nwargos.files.html Normal file
View file

@ -0,0 +1,9 @@
<html>
<title>nwArgos file structure</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS molecular dynamics simulations file structure</em></h1>
<hr>
<p>
File structure
</body>
</html>

24
doc/nwahtml/nwargos.html Normal file
View file

@ -0,0 +1,24 @@
<html>
<head>
<title>nwArgos molecular dynamics simulations</title>
</head>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS molecular dynamics simulations</em></h1>
<hr>
<em>nwARGOS</em> is the module in <em>NWChem</em> for molecular dynamics simulations of
macromolecular, liquid, and solution systems. This document provides a
description for this module.
<p>
<ul>
<li><a href="nwargos_intro.html">Introduction</a>
<li><a href="nwargos_funct.html">Functionality</a>
<li><a href="nwargos_files.html">File structure</a>
<li><a href="nwargos_imple.html">Parallel implementation</a>
<li><a href="nwargos_tutor.html">Tutorial</a>
<li><a href="nwargos_xmpls.html">Examples</a>
<li><a href="nwargos_bmrks.html">Benchmarks</a>
</ul>
<p>
<hr>
</body>
</html>

44
doc/nwahtml/nwargos_bmrks.html Normal file
View file

@ -0,0 +1,44 @@
<html>
<title>nwArgos benchmarks</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS benchmarks</em></h1>
<hr>
<h2>SPC/E water</h2>
Input files for molecular dynamics simulations of pure water are available for five different
system sizes. These systems were chosen to contain 1, 8, 27, 64 and 125 identical boxes of
216 SPC/E water molecules. Since the velocities are also identical in each box, the results
of a molecular dynamics simulation should be identical for each of these systems. This not
only provides a means of checking proper execution of the code, but also allows for
timings as a function of system size.
<p>
<a href="nwargos_bmrks_drop.html"><b>drop</b></a>: a molecular dynamics simulation of 216 SPC/E water molecules
<p>
<a href="nwargos_bmrks_bucket.html"><b>bucket</b></a>: a molecular dynamics simulation of 1,728 SPC/E water molecules
<p>
<a href="nwargos_bmrks_river.html"><b>river</b></a>: a molecular dynamics simulation of 5,832 SPC/E water molecules
<p>
<a href="nwargos_bmrks_sea.html"><b>sea</b></a>: a molecular dynamics simulation of 13,824 SPC/E water molecules
<p>
<a href="nwargos_bmrks_ocean.html"><b>ocean</b></a>: a molecular dynamics simulation of 27,000 SPC/E water molecules
<p>
<hr>
<h2>Myoglobin</h2>
<p>
As an example of a solvated protein, input files for myoglobin in aqueous solution are
available. This system has been used previously in the literature to benchmark parallel
molecular dynamics codes.
<p>
<a href="nwargos_bmrks_myo.html"><b>myo</b></a>: a molecular dynamics simulation of myoglobin in SPC/E water (10,914 atoms)
<p>
<hr>
<hr>
<h2>Speedup curves</h2>
<p>
For selected benchmarks speedup curves are compared as obtained for the
<a href="nwargos_bmrks_water_ksr.html">KSR-2</a> and the
<a href="nwargos_bmrks_water_sp2.html">IBM SP-2</a>.
<p>
<hr>
</body>
</html>

159
doc/nwahtml/nwargos_bmrks_bucket.html Normal file
View file

@ -0,0 +1,159 @@
<html>
<title>nwArgos bucket benchmark</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS <b>bucket</b> benchmark</em></h1>
<hr>
<h2>Molecular dynamics simulation of 1,728 SPC/E water molecules</h2>
Timings are given for a molecular dynamics simulation of 1,728 SPC/E water molecules
subject to periodic boundary conditions, in the NVT ensemble. These timings were
obtained from simulations of 1000 steps, and reflect the wall-clock time of a
single molecular dynamics step. The setup time and time for periodic recording of
coordinates and velocities is not included.
<p>
<table>
<tr>
<th></th>
<th>KSR-2</th>
<th>IBM SP-2</th>
</tr>
<tr>
<td>
4 nodes
</td>
<td>
1.695529
</td>
<td>
</td>
</tr>
<tr>
<td>
8 nodes
</td>
<td>
0.835476
</td>
<td>
</td>
</tr>
<tr>
<td>
16 nodes
</td>
<td>
0.448117
</td>
<td>
</td>
</tr>
<tr>
<td>
32 nodes
</td>
<td>
0.275099
</td>
<td>
</td>
</tr>
<tr>
<td>
64 nodes
</td>
<td>
0.203467
</td>
<td>
</td>
</tr>
</table>
<hr>
Speedups relative to the 4 node timings
<table>
<p>
<table>
<tr>
<th></th>
<th>KSR-2</th>
<th>IBM SP-2</th>
</tr>
<tr>
<td>
4 nodes
</td>
<td>
4.0
</td>
<td>
</td>
</tr>
<tr>
<td>
8 nodes
</td>
<td>
8.1
</td>
<td>
</td>
</tr>
<tr>
<td>
16 nodes
</td>
<td>
15.1
</td>
<td>
</td>
</tr>
<tr>
<td>
32 nodes
</td>
<td>
24.7
</td>
<td>
</td>
</tr>
<tr>
<td>
64 nodes
</td>
<td>
33.3
</td>
<td>
</td>
</tr>
</table>
<p>
<hr>
</body>
</html>

158
doc/nwahtml/nwargos_bmrks_drop.html Normal file
View file

@ -0,0 +1,158 @@
<html>
<title>nwArgos drop benchmark</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS <b>drop</b> benchmark</em></h1>
<hr>
<h2>Molecular dynamics simulation of 216 SPC/E water molecules</h2>
Timings are given for a molecular dynamics simulation of 216 SPC/E water molecules
subject to periodic boundary conditions, in the NVT ensemble. These timings were
obtained from simulations of 1000 steps, and reflect the wall-clock time of a
single molecular dynamics step. The setup time and time for periodic recording of
coordinates and velocities is not included.
<p>
<table>
<tr>
<th></th>
<th>KSR-2</th>
<th>IBM SP-2</th>
</tr>
<tr>
<td>
4 nodes
</td>
<td>
0.294088
</td>
<td>
</td>
</tr>
<tr>
<td>
8 nodes
</td>
<td>
0.165577
</td>
<td>
</td>
</tr>
<tr>
<td>
16 nodes
</td>
<td>
0.101206
</td>
<td>
</td>
</tr>
<tr>
<td>
32 nodes
</td>
<td>
0.110004
</td>
<td>
</td>
</tr>
<tr>
<td>
64 nodes
</td>
<td>
0.181529
</td>
<td>
</td>
</tr>
</table>
<hr>
Speedups relative to the 4 node timings
<table>
<p>
<table>
<tr>
<th></th>
<th>KSR-2</th>
<th>IBM SP-2</th>
</tr>
<tr>
<td>
4 nodes
</td>
<td>
4.0
</td>
<td>
</td>
</tr>
<tr>
<td>
8 nodes
</td>
<td>
7.1
</td>
<td>
</td>
</tr>
<tr>
<td>
16 nodes
</td>
<td>
11.6
</td>
<td>
</td>
</tr>
<tr>
<td>
32 nodes
</td>
<td>
10.7
</td>
<td>
</td>
</tr>
<tr>
<td>
64 nodes
</td>
<td>
6.5
</td>
<td>
</td>
</tr>
</table>
<p>
<hr>
</body>
</html>

123
doc/nwahtml/nwargos_bmrks_ocean.html Normal file
View file

@ -0,0 +1,123 @@
<html>
<title>nwArgos ocean benchmark</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS <b>ocean</b> benchmark</em></h1>
<hr>
<h2>Molecular dynamics simulation of 27,000 SPC/E water molecules</h2>
Timings are given for a molecular dynamics simulation of 27,000 SPC/E water molecules
subject to periodic boundary conditions, in the NVT ensemble. These timings were
obtained from simulations of 1000 steps, and reflect the wall-clock time of a
single molecular dynamics step. The setup time and time for periodic recording of
coordinates and velocities is not included.
<p>
<table>
<tr>
<th></th>
<th>KSR-2</th>
<th>IBM SP-2</th>
</tr>
<tr>
<th></th>
<th>Rc=0.9</th>
<th>Rc=0.9</th>
</tr>
<tr>
<td>4 nodes</td>
<td></td>
<td>15.035754</td>
</tr>
<tr>
<td>8 nodes</td>
<td></td>
<td>7.290162</td>
</tr>
<tr>
<td>20 nodes</td>
<td></td>
<td>2.717282</td>
</tr>
<tr>
<td>32 nodes</td>
<td></td>
<td>2.766097</td>
</tr>
<tr>
<td>50 nodes</td>
<td></td>
<td>1.472683</td>
</tr>
<tr>
<td>125 nodes</td>
<td></td>
<td>1.107691</td>
</tr>
</table>
<hr>
Speedups relative to the 4 node timings
<table>
<p>
<table>
<tr>
<th></th>
<th>KSR-2</th>
<th>IBM SP-2</th>
</tr>
<tr>
<th></th>
<th>Rc=0.9</th>
<th>Rc=0.9</th>
</tr>
<tr>
<td>4 nodes</td>
<td></td>
<td>4.0</td>
</tr>
<tr>
<td>8 nodes</td>
<td></td>
<td>8.3</td>
</tr>
<tr>
<td>20 nodes</td>
<td></td>
<td>22.1</td>
</tr>
<tr>
<td>32 nodes</td>
<td></td>
<td>21.7</td>
</tr>
<tr>
<td>50 nodes</td>
<td></td>
<td>40.8</td>
</tr>
<tr>
<td>125 nodes</td>
<td></td>
<td>54.3</td>
</tr>
</table>
<p>
<hr>
</body>
</html>

135
doc/nwahtml/nwargos_bmrks_river.html Normal file
View file

@ -0,0 +1,135 @@
<html>
<title>nwArgos river benchmark</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS <b>river</b> benchmark </em></h1>
<hr>
<h2>Molecular dynamics simulation of 5,832 SPC/E water molecules</h2>
Timings are given for a molecular dynamics simulation of 5,832 SPC/E water molecules
subject to periodic boundary conditions, in the NVT ensemble. These timings were
obtained from simulations of 1000 steps, and reflect the wall-clock time of a
single molecular dynamics step. The setup time and time for periodic recording of
coordinates and velocities is not included.
<p>
<table>
<tr>
<th></th>
<th>KSR-2</th>
<th>IBM SP-2</th>
</tr>
<tr>
<td>
4 nodes
</td>
<td>
6.118019
</td>
<td>
3.023760
</td>
</tr>
<tr>
<td>
8 nodes
</td>
<td>
2.866662
</td>
<td>
1.664759
</td>
</tr>
<tr>
<td>
27 nodes
</td>
<td>
0.889270
</td>
<td>
</td>
</tr>
<tr>
<td>
72 nodes
</td>
<td>
0.408092
</td>
<td>
</td>
</tr>
</table>
<hr>
Speedups relative to the 4 node timings
<table>
<p>
<table>
<tr>
<th></th>
<th>KSR-2</th>
<th>IBM SP-2</th>
</tr>
<tr>
<td>
4 nodes
</td>
<td>
4.0
</td>
<td>
4.0
</td>
</tr>
<tr>
<td>
8 nodes
</td>
<td>
8.5
</td>
<td>
7.3
</td>
</tr>
<tr>
<td>
27 nodes
</td>
<td>
27.5
</td>
<td>
</td>
</tr>
<tr>
<td>
72 nodes
</td>
<td>
60.0
</td>
<td>
</td>
</tr>
</table>
<p>
<hr>
</body>
</html>

138
doc/nwahtml/nwargos_bmrks_sea.html Normal file
View file

@ -0,0 +1,138 @@
<html>
<title>nwArgos sea benchmark</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS <b>sea</b> benchmark</em></h1>
<hr>
<h2>Molecular dynamics simulation of 13,824 SPC/E water molecules</h2>
Timings are given for a molecular dynamics simulation of 13,824 SPC/E water molecules
subject to periodic boundary conditions, in the NVT ensemble. These timings were
obtained from simulations of 1000 steps, and reflect the wall-clock time of a
single molecular dynamics step. The setup time and time for periodic recording of
coordinates and velocities is not included.
<p>
<table>
<tr>
<th></th>
<th>KSR-2</th>
<th>IBM SP-2</th>
<th>IBM SP-2</th>
</tr>
<tr>
<th></th>
<th>Rc=0.9</th>
<th>Rc=0.9</th>
<th>Rc=1.8</th>
</tr>
<tr>
<td>4 nodes</td>
<td>15.117976</td>
<td>7.331969</td>
<td>52.237927</td>
</tr>
<tr>
<td>8 nodes</td>
<td>7.169106</td>
<td>3.816244</td>
<td>27.631083</td>
</tr>
<tr>
<td>16 nodes</td>
<td>3.472468</td>
<td>2.130735</td>
<td>13.496562</td>
</tr>
<tr>
<td>32 nodes</td>
<td>1.782187</td>
<td></td>
<td>6.811522</td>
</tr>
<tr>
<td>64 nodes</td>
<td>0.921344</td>
<td>1.007676</td>
<td>3.663068</td>
</tr>
<tr>
<td>128 nodes</td>
<td></td>
<td></td>
<td>2.280681</td>
</tr>
</table>
<hr>
Speedups relative to the 4 node timings
<table>
<p>
<table>
<tr>
<th></th>
<th>KSR-2</th>
<th>IBM SP-2</th>
</tr>
<tr>
<th></th>
<th>Rc=0.9</th>
<th>Rc=0.9</th>
<th>Rc=1.8</th>
</tr>
<tr>
<td>4 nodes</td>
<td>4.0</td>
<td>4.0</td>
<td>4.0</td>
</tr>
<tr>
<td>8 nodes</td>
<td>8.5</td>
<td>8.0</td>
<td>7.6</td>
</tr>
<tr>
<td>16 nodes</td>
<td>17.4</td>
<td>14.5</td>
<td>15.5</td>
</tr>
<tr>
<td>32 nodes</td>
<td>33.9</td>
<td>25.9</td>
<td>36.0</td>
</tr>
<tr>
<td>64 nodes</td>
<td>65.6</td>
<td>30.1</td>
<td>57.1</td>
</tr>
<tr>
<td>128 nodes</td>
<td></td>
<td></td>
<td>91.6</td>
</tr>
</table>
<p>
<hr>
</body>
</html>

9
doc/nwahtml/nwargos_bmrks_water_ksr.html Normal file
View file

@ -0,0 +1,9 @@
<html>
<title>nwArgos KSR-2 benchmarks</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS KSR-2 benchmarks</em></h1>
<hr>
<IMG ALIGN=top SRC="nwargos_sppedup_ksr2.gif">
<hr>
</body>
</html>

9
doc/nwahtml/nwargos_bmrks_water_sp2.html Normal file
View file

@ -0,0 +1,9 @@
<html>
<title>nwArgos IBM SP-2 benchmarks</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS IBM SP-2 benchmarks</em></h1>
<hr>
<IMG ALIGN=top SRC="nwargos_speedup_sp2.gif">
<hr>
</body>
</html>

63
doc/nwahtml/nwargos_crown.html Normal file
View file

@ -0,0 +1,63 @@
<html>
<title>nwArgos example: crown</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS example: crown</em></h1>
<hr>
<p>
This example goes through the complete sequence of steps to perform a
free energy difference simulation in which Na+ is mutated into K+,
complexed to the crown ether 18C6, in aqueous solution.
<p>
<ol>
<li>
The crown ether wil be built from CH2-O-CH2 fragments. This fragment
is not part of the standard segment database. Also a corresponding fragment
is not part of the fragment library. The fragment is created using an
editor, and should be named
<a href="nwargos_crown_frg.html">coc_______.frg</a>.
<p>
<li>
The fragment just created is force field independent. To create the
force field <b>amber</b> dependent segment file, give the command
<p>
<tt>nwsgm coc_______ amber</tt>
<p>
This command searches the fragment libraries and the local file
<b>coc_______.frg</b> for a fragment entry <tt>$coc</tt>.
The generic atom types defined in the fragment are substituted for
the <b>amber</b> atom types. The translation tables are found in
the atom type translation library files or the local file
<b>coc_______.att</b>, if present.
A segment file <a href="nwargos_crown_sgm.html">coc_______.sgm</a>
is created that should be renamed to <b>crown.sgm</b>.
Alternatively, this file may be appended to
<b>amber_u.sgm</b> or <b>amber_r.sgm</b>, provided that these library
files are defined in the file <b>$HOME/.nwargos</b>.
<p>
<li>
A sequence file needs to be created, defining the molecular system
in terms of segments. Using an editor create the file
<a href="nwargos_crown_seq.html">crown.seq</a>. This file defines
the 18C6 crown ether in terms of six cyclicly arranged <tt>coc</tt>
fragments. It also specifies the solvent as the SPC/E water model.
<p>
<li>
The topology file <a href="nwargos_crown_top.html">crown.top</a> is
created, giving the command
<p>
<tt>nwtop crown amber</tt>
<p>
This command searches the <b>amber</b> sequence database files, and
the local sequence file <b>crown.seq</b> for a sequence <tt>crown</tt>.
The force field needs to be given in order to search the correct
database files. If the sequence is found, it searches the <b>amber</b>
segment databases and the local segment file <b>crown.sgm</b> for all
segments specified in the sequence. When all segments have been found,
the topology is generated using the rules appropriate for the force
field. All parameters not explicitly given in the segment are added
from the <b>amber</b> parameter library files, and the local file
<b>crown.par</b> if present. Any segments or parameters not found
can be supplied in the local files.
</ol>
</body>
</html>

27
doc/nwahtml/nwargos_crown_frg.html Normal file
View file

@ -0,0 +1,27 @@
<html>
<title>nwArgos example: crown: coc fragment file</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS example: crown: coc fragment file</em></h1>
<hr>
<p>
<pre>
$coc
7 0 0
1C1 CT 1 0 1 1 0.000000
2H11 H1 0 0 1 1 0.150000
3H12 H1 0 0 1 1 0.150000
4O OS 0 0 1 1 -0.600000
5C2 CT 2 0 1 1 0.000000
6H21 H1 0 0 1 1 0.150000
7H22 H1 0 0 1 1 0.150000
1 4 5
2 1 3
6 5 7
</pre>
<p>
<hr>
Note that the first atom (<tt>C1</tt>) is defined as first link
atom, and the fifth atom (<tt>C2</tt>) is defined as second link
atom.
</body>
</html>

29
doc/nwahtml/nwargos_crown_seq.html Normal file
View file

@ -0,0 +1,29 @@
<html>
<title>nwArgos example: crown: sequence file</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS example: crown: sequence file</em></h1>
<hr>
<p>
<pre>
$crown
1coc
2coc
3coc
4coc
5coc
6coc 0 0 1 1
-2
0SPCE
-3
</pre>
<p>
<hr>
Note that the sixth <tt>coc</tt> segment's second link is pointing
to the first link atom of the first <tt>coc</tt> segment, to make
the cyclic crown ether. Alternatively this could have been specified
by letting the first <tt>coc</tt> segment's first link point to the
sixth <tt>coc</tt> segment's second link atom. The other <tt>coc</tt>
segments are automatically link their first link atom to their previous
segment's second link atom.
</body>
</html>

62
doc/nwahtml/nwargos_crown_sgm.html Normal file
View file

@ -0,0 +1,62 @@
<html>
<title>nwArgos example: crown: coc fragment file</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS example: crown: coc fragment file</em></h1>
<hr>
<p>
<pre>
$coc
7 6 7 4 0
1C1 CT CT CT 1 1 1 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2H11 H H H 1 1 0 0
0.150000 0.000000 0.150000 0.000000 0.150000 0.000000
3H12 H H H 1 1 0 0
0.150000 0.000000 0.150000 0.000000 0.150000 0.000000
4O O O O 1 1 0 0
-0.600000 0.000000 -0.600000 0.000000 -0.600000 0.000000
5C2 CT CT CT 1 1 2 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
6H21 H H H 1 1 0 0
0.150000 0.000000 0.150000 0.000000 0.150000 0.000000
7H22 H H H 1 1 0 0
0.150000 0.000000 0.150000 0.000000 0.150000 0.000000
1 1 2 0 0
0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00
2 1 3 0 0
0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00
3 1 4 0 0
0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00
4 4 5 0 0
0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00
5 5 6 0 0
0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00
6 5 7 0 0
0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00
1 2 1 3 0 0
0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00
2 2 1 4 0 0
0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00
3 3 1 4 0 0
0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00
4 1 4 5 0 0
0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00
5 4 5 6 0 0
0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00
6 4 5 7 0 0
0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00
7 6 5 7 0 0
0.000000 0.00000E+00 0.000000 0.00000E+00 0.000000 0.00000E+00
1 2 1 4 5 0 0
0 0.000000 0.00000E+00 0 0.000000 0.00000E+00 0 0.000000 0.00000E+00
2 3 1 4 5 0 0
0 0.000000 0.00000E+00 0 0.000000 0.00000E+00 0 0.000000 0.00000E+00
3 1 4 5 6 0 0
0 0.000000 0.00000E+00 0 0.000000 0.00000E+00 0 0.000000 0.00000E+00
4 1 4 5 7 0 0
0 0.000000 0.00000E+00 0 0.000000 0.00000E+00 0 0.000000 0.00000E+00
</pre>
<p>
<hr>
</body>
</html>

665
doc/nwahtml/nwargos_crown_top.html Normal file
View file

@ -0,0 +1,665 @@
<html>
<title>nwArgos example: crown: topology file</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS example: crown: topology file</em></h1>
<hr>
<p>
<pre>
nwArgos test topology
generated by nwtop
test
0 amber
5
OW w 15.999400OW w 15.999400OW w 15.999400
HW w 1.008000HW w 1.008000HW w 1.008000
CT 12.011000CT 12.011000CT 12.011000
H2 1.007940H2 1.007940H2 1.007940
OS 15.999400OS 15.999400OS 15.999400
0.24887E-02 0.24887E-02 0.24887E-02 0.12444E-02 0.12444E-02 0.12444E-02
0.24348E-05 0.24348E-05 0.24348E-05 0.12174E-05 0.12174E-05 0.12174E-05
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.26639E-02 0.26639E-02 0.26639E-02 0.13319E-02 0.13319E-02 0.13319E-02
0.32882E-05 0.32882E-05 0.32882E-05 0.16441E-05 0.16441E-05 0.16441E-05
0.33252E-03 0.33252E-03 0.33252E-03 0.16626E-03 0.16626E-03 0.16626E-03
0.13524E-06 0.13524E-06 0.13524E-06 0.67620E-07 0.67620E-07 0.67620E-07
0.22764E-02 0.22764E-02 0.22764E-02 0.11382E-02 0.11382E-02 0.11382E-02
0.19260E-05 0.19260E-05 0.19260E-05 0.96298E-06 0.96298E-06 0.96298E-06
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
0.28268E-02 0.28268E-02 0.28268E-02 0.14134E-02 0.14134E-02 0.14134E-02
0.43642E-05 0.43642E-05 0.43642E-05 0.21821E-05 0.21821E-05 0.21821E-05
0.36890E-03 0.36890E-03 0.36890E-03 0.18445E-03 0.18445E-03 0.18445E-03
0.19620E-06 0.19620E-06 0.19620E-06 0.98100E-07 0.98100E-07 0.98100E-07
0.24503E-02 0.24503E-02 0.24503E-02 0.12251E-02 0.12251E-02 0.12251E-02
0.26302E-05 0.26302E-05 0.26302E-05 0.13151E-05 0.13151E-05 0.13151E-05
0.38210E-04 0.38210E-04 0.38210E-04 0.19105E-04 0.19105E-04 0.19105E-04
0.55564E-08 0.55564E-08 0.55564E-08 0.27782E-08 0.27782E-08 0.27782E-08
0.29717E-03 0.29717E-03 0.29717E-03 0.14859E-03 0.14859E-03 0.14859E-03
0.10213E-06 0.10213E-06 0.10213E-06 0.51063E-07 0.51063E-07 0.51063E-07
0.20747E-02 0.20747E-02 0.20747E-02 0.10374E-02 0.10374E-02 0.10374E-02
0.15125E-05 0.15125E-05 0.15125E-05 0.75626E-06 0.75626E-06 0.75626E-06
3 3 0 0 0 0 0
42 42 78 108 0 90 210
1 0 0 0 0SPCE MOW 1
-0.847600 -0.847600 -0.847600 0.000000 0.000000 0.000000
2 0 0 0 0SPCE MHW 2
0.423800 0.423800 0.423800 0.000000 0.000000 0.000000
2 0 0 0 0SPCE MHW 3
0.423800 0.423800 0.423800 0.000000 0.000000 0.000000
1 2 1 1
0.100000 0.00000E+00 0.100000 0.00000E+00 0.100000 0.00000E+00
1 3 1 2
0.100000 0.00000E+00 0.100000 0.00000E+00 0.100000 0.00000E+00
2 3 1 3
0.163333 0.00000E+00 0.163333 0.00000E+00 0.163333 0.00000E+00
3 1 1 1 1coc C1 1 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 1 1 1 1coc H11 2 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
4 1 1 1 1coc H12 3 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
5 1 1 1 1coc O 4 0
-0.600000 -0.600000 -0.600000 0.000000 0.000000 0.000000
3 1 1 1 1coc C2 5 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 1 1 1 1coc H21 6 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
4 1 1 1 1coc H22 7 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
3 1 2 2 2coc C1 8 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 1 2 2 2coc H11 9 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
4 1 2 2 2coc H12 10 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
5 1 2 2 2coc O 11 0
-0.600000 -0.600000 -0.600000 0.000000 0.000000 0.000000
3 1 2 2 2coc C2 12 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 1 2 2 2coc H21 13 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
4 1 2 2 2coc H22 14 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
3 1 3 3 3coc C1 15 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 1 3 3 3coc H11 16 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
4 1 3 3 3coc H12 17 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
5 1 3 3 3coc O 18 0
-0.600000 -0.600000 -0.600000 0.000000 0.000000 0.000000
3 1 3 3 3coc C2 19 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 1 3 3 3coc H21 20 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
4 1 3 3 3coc H22 21 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
3 1 4 4 4coc C1 22 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 1 4 4 4coc H11 23 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
4 1 4 4 4coc H12 24 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
5 1 4 4 4coc O 25 0
-0.600000 -0.600000 -0.600000 0.000000 0.000000 0.000000
3 1 4 4 4coc C2 26 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 1 4 4 4coc H21 27 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
4 1 4 4 4coc H22 28 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
3 1 5 5 5coc C1 29 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 1 5 5 5coc H11 30 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
4 1 5 5 5coc H12 31 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
5 1 5 5 5coc O 32 0
-0.600000 -0.600000 -0.600000 0.000000 0.000000 0.000000
3 1 5 5 5coc C2 33 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 1 5 5 5coc H21 34 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
4 1 5 5 5coc H22 35 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
3 1 6 6 6coc C1 36 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 1 6 6 6coc H11 37 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
4 1 6 6 6coc H12 38 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
5 1 6 6 6coc O 39 0
-0.600000 -0.600000 -0.600000 0.000000 0.000000 0.000000
3 1 6 6 6coc C2 40 0
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4 1 6 6 6coc H21 41 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
4 1 6 6 6coc H22 42 0
0.150000 0.150000 0.150000 0.000000 0.000000 0.000000
1 2 1 1
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
1 3 1 2
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
1 4 0 3
0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06
4 5 0 4
0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06
5 6 1 5
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
5 7 1 6
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
8 9 1 7
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
8 10 1 8
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
8 11 0 9
0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06
11 12 0 10
0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06
12 13 1 11
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
12 14 1 12
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
8 5 0 13
0.152600 0.25940E+06 0.152600 0.25940E+06 0.152600 0.25940E+06
15 16 1 14
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
15 17 1 15
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
15 18 0 16
0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06
18 19 0 17
0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06
19 20 1 18
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
19 21 1 19
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
15 12 0 20
0.152600 0.25940E+06 0.152600 0.25940E+06 0.152600 0.25940E+06
22 23 1 21
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
22 24 1 22
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
22 25 0 23
0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06
25 26 0 24
0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06
26 27 1 25
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
26 28 1 26
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
22 19 0 27
0.152600 0.25940E+06 0.152600 0.25940E+06 0.152600 0.25940E+06
29 30 1 28
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
29 31 1 29
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
29 32 0 30
0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06
32 33 0 31
0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06
33 34 1 32
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
33 35 1 33
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
29 26 0 34
0.152600 0.25940E+06 0.152600 0.25940E+06 0.152600 0.25940E+06
36 37 1 35
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
36 38 1 36
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
36 39 0 37
0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06
39 40 0 38
0.141000 0.26778E+06 0.141000 0.26778E+06 0.141000 0.26778E+06
40 41 1 39
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
40 42 1 40
0.109000 0.28452E+06 0.109000 0.28452E+06 0.109000 0.28452E+06
36 33 0 41
0.152600 0.25940E+06 0.152600 0.25940E+06 0.152600 0.25940E+06
40 1 0 42
0.152600 0.25940E+06 0.152600 0.25940E+06 0.152600 0.25940E+06
2 1 3 0 1
1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03
2 1 4 0 2
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
3 1 4 0 3
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
1 4 5 0 4
1.911140 0.50208E+03 1.911140 0.50208E+03 1.911140 0.50208E+03
4 5 6 0 5
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
4 5 7 0 6
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
6 5 7 0 7
1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03
9 8 10 0 8
1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03
9 8 11 0 9
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
10 8 11 0 10
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
8 11 12 0 11
1.911140 0.50208E+03 1.911140 0.50208E+03 1.911140 0.50208E+03
11 12 13 0 12
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
11 12 14 0 13
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
13 12 14 0 14
1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03
9 8 5 0 15
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
10 8 5 0 16
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
11 8 5 0 17
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
4 5 8 0 18
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
6 5 8 0 19
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
7 5 8 0 20
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
16 15 17 0 21
1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03
16 15 18 0 22
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
17 15 18 0 23
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
15 18 19 0 24
1.911140 0.50208E+03 1.911140 0.50208E+03 1.911140 0.50208E+03
18 19 20 0 25
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
18 19 21 0 26
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
20 19 21 0 27
1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03
16 15 12 0 28
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
17 15 12 0 29
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
18 15 12 0 30
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
11 12 15 0 31
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
13 12 15 0 32
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
14 12 15 0 33
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
23 22 24 0 34
1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03
23 22 25 0 35
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
24 22 25 0 36
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
22 25 26 0 37
1.911140 0.50208E+03 1.911140 0.50208E+03 1.911140 0.50208E+03
25 26 27 0 38
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
25 26 28 0 39
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
27 26 28 0 40
1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03
23 22 19 0 41
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
24 22 19 0 42
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
25 22 19 0 43
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
18 19 22 0 44
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
20 19 22 0 45
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
21 19 22 0 46
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
30 29 31 0 47
1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03
30 29 32 0 48
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
31 29 32 0 49
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
29 32 33 0 50
1.911140 0.50208E+03 1.911140 0.50208E+03 1.911140 0.50208E+03
32 33 34 0 51
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
32 33 35 0 52
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
34 33 35 0 53
1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03
30 29 26 0 54
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
31 29 26 0 55
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
32 29 26 0 56
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
25 26 29 0 57
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
27 26 29 0 58
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
28 26 29 0 59
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
37 36 38 0 60
1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03
37 36 39 0 61
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
38 36 39 0 62
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
36 39 40 0 63
1.911140 0.50208E+03 1.911140 0.50208E+03 1.911140 0.50208E+03
39 40 41 0 64
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
39 40 42 0 65
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
41 40 42 0 66
1.911140 0.29288E+03 1.911140 0.29288E+03 1.911140 0.29288E+03
37 36 33 0 67
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
38 36 33 0 68
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
39 36 33 0 69
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
32 33 36 0 70
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
34 33 36 0 71
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
35 33 36 0 72
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
39 40 1 0 73
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
41 40 1 0 74
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
42 40 1 0 75
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
2 1 40 0 76
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
3 1 40 0 77
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
4 1 40 0 78
1.911140 0.41840E+03 1.911140 0.41840E+03 1.911140 0.41840E+03
2 1 4 5 0 1
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
3 1 4 5 0 2
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
1 4 5 6 0 3
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
1 4 5 7 0 4
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
9 8 11 12 0 5
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
10 8 11 12 0 6
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
8 11 12 13 0 7
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
8 11 12 14 0 8
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
4 5 8 9 0 9
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
6 5 8 9 0 10
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
7 5 8 9 0 11
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
4 5 8 10 0 12
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
6 5 8 10 0 13
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
7 5 8 10 0 14
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
5 8 11 12 0 15
3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01
5 8 11 12 0 15
2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00
4 5 8 11 0 16
3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00
4 5 8 11 0 16
2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01
6 5 8 11 0 17
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
7 5 8 11 0 18
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
1 4 5 8 0 19
3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01
1 4 5 8 0 19
2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00
40 1 4 5 0 20
3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01
40 1 4 5 0 20
2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00
16 15 18 19 0 21
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
17 15 18 19 0 22
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
15 18 19 20 0 23
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
15 18 19 21 0 24
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
11 12 15 16 0 25
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
13 12 15 16 0 26
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
14 12 15 16 0 27
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
11 12 15 17 0 28
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
13 12 15 17 0 29
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
14 12 15 17 0 30
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
12 15 18 19 0 31
3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01
12 15 18 19 0 31
2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00
11 12 15 18 0 32
3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00
11 12 15 18 0 32
2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01
13 12 15 18 0 33
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
14 12 15 18 0 34
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
8 11 12 15 0 35
3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01
8 11 12 15 0 35
2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00
23 22 25 26 0 36
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
24 22 25 26 0 37
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
22 25 26 27 0 38
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
22 25 26 28 0 39
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
18 19 22 23 0 40
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
20 19 22 23 0 41
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
21 19 22 23 0 42
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
18 19 22 24 0 43
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
20 19 22 24 0 44
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
21 19 22 24 0 45
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
19 22 25 26 0 46
3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01
19 22 25 26 0 46
2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00
18 19 22 25 0 47
3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00
18 19 22 25 0 47
2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01
20 19 22 25 0 48
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
21 19 22 25 0 49
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
15 18 19 22 0 50
3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01
15 18 19 22 0 50
2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00
30 29 32 33 0 51
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
31 29 32 33 0 52
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
29 32 33 34 0 53
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
29 32 33 35 0 54
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
25 26 29 30 0 55
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
27 26 29 30 0 56
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
28 26 29 30 0 57
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
25 26 29 31 0 58
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
27 26 29 31 0 59
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
28 26 29 31 0 60
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
25 26 29 32 0 61
3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00
25 26 29 32 0 61
2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01
27 26 29 32 0 62
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
28 26 29 32 0 63
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
26 29 32 33 0 64
3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01
26 29 32 33 0 64
2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00
22 25 26 29 0 65
3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01
22 25 26 29 0 65
2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00
37 36 39 40 0 66
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
38 36 39 40 0 67
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
36 39 40 41 0 68
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
36 39 40 42 0 69
3 0.000000 0.16039E+01 3 0.000000 0.16039E+01 3 0.000000 0.16039E+01
32 33 36 37 0 70
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
34 33 36 37 0 71
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
35 33 36 37 0 72
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
32 33 36 38 0 73
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
34 33 36 38 0 74
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
35 33 36 38 0 75
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
32 33 36 39 0 76
3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00
32 33 36 39 0 76
2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01
34 33 36 39 0 77
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
35 33 36 39 0 78
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
33 36 39 40 0 79
3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01
33 36 39 40 0 79
2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00
1 4 5 8 0 80
3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01
1 4 5 8 0 80
2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00
2 1 40 39 0 81
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
3 1 40 39 0 82
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
4 1 40 39 0 83
3 0.000000 0.60249E+00 3 0.000000 0.60249E+00 3 0.000000 0.60249E+00
4 1 40 39 0 83
2 0.000000 0.41840E+01 2 0.000000 0.41840E+01 2 0.000000 0.41840E+01
2 1 40 41 0 84
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
3 1 40 41 0 85
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
4 1 40 41 0 86
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
2 1 40 42 0 87
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
3 1 40 42 0 88
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
4 1 40 42 0 89
3 0.000000 0.65084E+00 3 0.000000 0.65084E+00 3 0.000000 0.65084E+00
40 1 4 5 0 90
3 0.000000 0.16025E+01 3 0.000000 0.16025E+01 3 0.000000 0.16025E+01
40 1 4 5 0 90
2 3.141590 0.41840E+00 2 3.141590 0.41840E+00 2 3.141590 0.41840E+00
1 1 1 1 2 2 2 2 3 3 3
3 4 4 4 4 4 4 5 5 6 6
6 7 7 7 8 8 8 9 10 11 11
11 12 13 13 13 14 14 14 15 15 15
16 17 18 18 18 19 20 20 20 21 21
21 22 22 22 23 24 25 25 25 26 27
27 27 28 28 28 29 29 29 30 31 32
32 32 33 34 34 34 35 35 35 36 36
37 38
6 7 8 36 5 39 41 42 5 39 41
42 9 10 11 39 41 42 12 40 9 10
11 9 10 11 13 14 15 12 12 16 17
18 19 16 17 18 16 17 18 20 21 22
19 19 23 24 25 26 23 24 25 23 24
25 27 28 29 26 26 30 31 32 33 30
31 32 30 31 32 34 35 36 33 33 37
38 39 40 37 38 39 37 38 39 41 42
40 40
1 1 1 1 1 1 1 1 2 2 2
2 2 2 2 3 3 3 3 3 3 4
4 4 4 4 4 4 4 4 4 4 5
5 5 5 6 6 6 6 6 7 7 7
7 8 8 8 8 8 8 8 8 9 9
9 9 10 10 10 11 11 11 11 11 11
11 11 12 12 12 13 13 13 13 13 14
14 14 14 15 15 15 15 15 15 15 15
16 16 16 16 17 17 17 18 18 18 18
18 18 18 18 19 19 19 20 20 20 20
20 21 21 21 21 22 22 22 22 22 22
22 22 23 23 23 23 24 24 24 25 25
25 25 25 25 25 25 26 26 26 27 27
27 27 27 28 28 28 28 29 29 29 29
29 29 29 29 30 30 30 30 31 31 31
32 32 32 32 32 32 32 32 33 33 33
34 34 34 34 34 35 35 35 35 36 36
36 36 36 36 36 37 37 37 37 38 38
38 39 39 39 39 39 40 40 40 41 41
42
2 3 4 5 6 7 8 36 3 4 5
39 40 41 42 4 5 39 40 41 42 5
6 7 8 9 10 11 39 40 41 42 6
7 12 40 7 8 9 10 11 8 9 10
11 5 9 10 11 12 13 14 15 5 10
11 12 5 11 12 5 12 13 14 15 16
17 18 13 14 19 14 15 16 17 18 15
16 17 18 12 16 17 18 19 20 21 22
12 17 18 19 12 18 19 12 19 20 21
22 23 24 25 20 21 26 21 22 23 24
25 22 23 24 25 19 23 24 25 26 27
28 29 19 24 25 26 19 25 26 19 26
27 28 29 30 31 32 27 28 33 28 29
30 31 32 29 30 31 32 26 30 31 32
33 34 35 36 26 31 32 33 26 32 33
26 33 34 35 36 37 38 39 34 35 40
35 36 37 38 39 36 37 38 39 33 37
38 39 40 41 42 33 38 39 40 33 39
40 1 33 40 41 42 1 41 42 1 42
1
</pre>
<p>
<hr>
</body>
</html>

83
doc/nwahtml/nwargos_extensions.html Normal file
View file

@ -0,0 +1,83 @@
<html>
<title>nwArgos extensions</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS extensions</em></h1>
<hr>
<p>
<b><em>File extensions</em></b>
<p>
The following file extensions are used by <em>nwARGOS</em> and the setup
programs <a href="nwargos_nwTOP"><em>nwTOP</em></a>,
<a href="nwargos_nwRST"><em>nwRST</em></a> and
<a href="nwargos_nwSGM"><em>nwSGM</em></a>.
<p>
<table>
<tr>
<th>Extension</th>
<th>File description</th>
</tr>
<tr>
<td><b>coo</b></td><td> coordinate file</td>
</tr>
<tr>
<td><b>inp</b></td><td> input file</td>
</tr>
<tr>
<td><b>prp</b></td><td> property file</td>
</tr>
<tr>
<td><b>rin</b></td><td> <em>nwRST</em> input file</td>
</tr>
<tr>
<td><b>rou</b></td><td> <em>nwRST</em> output file</td>
</tr>
<tr>
<td><b>rst</b></td><td> restart file</td>
</tr>
<tr>
<td><b>seq</b></td><td> <em>nwTOP</em> sequence input file</td>
</tr>
<tr>
<td><b>sco</b></td><td> solute coordinate file</td>
</tr>
<tr>
<td><b>svl</b></td><td> solute velocity file</td>
</tr>
<tr>
<td><b>top</b></td><td> topology file</td>
</tr>
<tr>
<td><b>vel</b></td><td> velocity file</td>
</table>
<hr>
<p>
<b><em>Database extensions</em></b>
<p>
The following file extensions are used by the setup programs
<a href="nwargos_nwTOP"><em>nwTOP</em></a>,
<a href="nwargos_nwRST"><em>nwRST</em></a> and
<a href="nwargos_nwSGM"><em>nwSGM</em></a>.
<p>
<table>
<tr>
<th>Extension</th>
<th>File description</th>
</tr>
<tr>
<td><b>att</b></td><td> atom type database</td>
</tr>
<tr>
<td><b>frg</b></td><td> fragment database</td>
</tr>
<tr>
<td><b>par</b></td><td> parameter database</td>
</tr>
<tr>
<td><b>sgm</b></td><td> segment database</td>
</tr>
<tr>
<td><b>slv</b></td><td> solvent restart file</td>
</tr>
</table>
</body>
</html>

65
doc/nwahtml/nwargos_files.html Normal file
View file

@ -0,0 +1,65 @@
<html>
<title>nwArgos file structure</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS file structure</em></h1>
<hr>
<p>
<b><em>File names</em></b>
<p>
File names used by <em>nwARGOS</em> need to have the form
<b>project_id.ext</b>, with exception of the <a href="nwargos_topology.html">
topology</a> file, which should be named <b>project.top</b>, and the input
file for <em>NWChem</em>, which should simply be <b>project</b>.
Anything that refers to the definition of the chemical system can be used
for <b>project</b>, as long as no periods or underlines are used. <br>
The identifier <b>id</b> can be anything that refers to the type of calculation
to be performed for the system.<br>
The <a href="nwargos_extensions.html">extensions</a> <b>ext</b>
identify the kind of information on the file, and are determined by the
programs. Examples of extensions are <b>top</b> for the topology file,
<b>rst</b> for the restart file and <b>inp</b> for the input file.
<p>
This file naming convention allows for the creation of a single topology file
<b>project.top</b> for a chemical system with which a number of different
calculations, identified with different <b>id</b>.
<p>
<hr>
<p>
<b><em>Database names</em></b>
<p>
A similar convention is used to identify databases used by the setup programs
<a href="nwargos_nwTOP.html"><em>nwTOP</em></a>,
<a href="nwargos_nwRST.html"><em>nwRST</em></a> and
<a href="nwargos_nwSGM.html"><em>nwSGM</em></a>.
Force field database names have the form
<b>forcefield_level.ext</b>, where <b>forcefield</b> stands for any of the
<a href="nwargos_forcefields.html">supported force fields</a>. The source
of the data is identified by <b>level</b>, and can be
<p>
<table>
<tr>
<th>level</th><th>Description</th><th>Availability</th>
</tr>
<tr>
<td><b>s</b></td><td>original published data</td><td>public</td>
</tr>
<tr>
<td><b>x</b></td><td>additional published data</td><td>public</td>
</tr>
<tr>
<td><b>u</b></td><td>user preferred data</td><td>private</td>
</tr>
<tr>
<td><b>r</b></td><td>user defined run specific data</td><td>private</td>
</tr>
</table>
<p>
Only the level <b>s</b> and <b>x</b> databases are publicly available. The user is
responsible for the private level <b>u</b> and <b>r</b> databases.
<p>
Other database files include the force field independent fragment libraries and
the solvation restart files.
<p>
<hr>
</body>
</html>

35
doc/nwahtml/nwargos_forcefields.html Normal file
View file

@ -0,0 +1,35 @@
<html>
<title>nwArgos force fields</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS supported force fields</em></h1>
<hr>
<p>
Force fields supported by <em>nwARGOS</em> are
<p>
<table>
<tr>
<th>Keyword</th><th>Force field name</th><th>Current status</th>
</tr>
<tr>
<td><b>amber</b></td><td> AMBER4.0</td><td>available</td>
</tr>
<tr>
<td><b>charmm</b></td><td> CHARMM</td><td>planned</td>
</tr>
<tr>
<td><b>cvff</b></td><td> CVFF</td><td>planned</td>
</tr>
<tr>
<td><b>gromos</b></td><td> GROMOS87</td><td>planned</td>
</tr>
<tr>
<td><b>oplsa</b></td><td> OPLS/AMBER3.0</td><td>planned</td>
</tr>
<tr>
<td><b>oplsg</b></td><td> OPLS/GROMOS87</td><td>planned</td>
</tr>
</table>
<p>
<hr>
</body>
</html>

9
doc/nwahtml/nwargos_funct.html Normal file
View file

@ -0,0 +1,9 @@
<html>
<title>nwArgos functionality</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS molecular dynamics simulations functionality</em></h1>
<hr>
<p>
Functionality
</body>
</html>

9
doc/nwahtml/nwargos_imple.html Normal file
View file

@ -0,0 +1,9 @@
<html>
<title>nwArgos parallel implementation</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS molecular dynamics simulations parallel implementation</em></h1>
<hr>
<p>
Parallel implementation
</body>
</html>

325
doc/nwahtml/nwargos_input.html Normal file
View file

@ -0,0 +1,325 @@
<html>
<title>nwArgos input</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS input</em></h1>
<hr>
<p>
<b><em>Input file format</em></b>
<p>
The input file <b>project_id.inp</b> determines the type of calculation
to be performed. Details of the calculation are given in keyworded
format.
<hr>
<b><em>Input file keywords</em></b>
<p>
Keywords need to be given exactly as given below. Numeric values are
in free format. Keywords recognized include
<p>
<b><tt>#</tt></b> <br>
Any card in the input file that starts with the number sign (#) is
treated as a comment, and ignored.
<p>
<b><tt> </tt></b> <br>
Any card in the input file that starts with a space is
treated as a comment, and ignored.
<p>
<b><tt>Title</tt></b> <br>
Three title cards (a) and one with date and time (2a10) are read.
<p>
<b><tt>Task SP</tt></b> <br>
Identifies that a single point energy evaluation is to be done using
parameters from set 1.
This card cancels any previous <b><tt>Task</tt></b> cards in the input
deck.
<p>
<b><tt>Task SP set 2</tt></b> <br>
Identifies that a single point energy evaluation is to be done using
parameters from set 2.
This card cancels any previous <b><tt>Task</tt></b> cards in the input
deck.
<p>
<b><tt>Task SP set 3</tt></b> <br>
Identifies that a single point energy evaluation is to be done using
parameters from set 3.
This card cancels any previous <b><tt>Task</tt></b> cards in the input
deck.
<p>
<b><tt>Task MD</tt></b> <br>
Identifies that a molecular dynamics simulation is to be carried out using
parameters from set 1.
This card cancels any previous <b><tt>Task</tt></b> cards in the input
deck.
<p>
<b><tt>Task MD set 2</tt></b> <br>
Identifies that a molecular dynamics simulation is to be carried out using
parameters from set 2.
This card cancels any previous <b><tt>Task</tt></b> cards in the input
deck.
<p>
<b><tt>Task MD set 3</tt></b> <br>
Identifies that a molecular dynamics simulation is to be carried out using
parameters from set 3.
This card cancels any previous <b><tt>Task</tt></b> cards in the input
deck.
<p>
<b><tt>Task EM</tt></b> <br>
Identifies that an energy minimization is to be performed out using
parameters from set 1.
This card cancels any previous <b><tt>Task</tt></b> cards in the input
deck.
<p>
<b><tt>Task EM set 2</tt></b> <br>
Identifies that an energy minimization is to be performed out using
parameters from set 2.
This card cancels any previous <b><tt>Task</tt></b> cards in the input
deck.
<p>
<b><tt>Task EM set 3</tt></b> <br>
Identifies that an energy minimization is to be performed out using
parameters from set 3.
This card cancels any previous <b><tt>Task</tt></b> cards in the input
deck.
<p>
<b><tt>Task MCTI</tt></b> <br>
Identifies that a multiconfiguration thermodynamic integration
calculation will be carried out.
This card cancels any previous <b><tt>Task</tt></b> cards in the input
deck.
<p>
<b><tt>Start time</tt></b> <em>rvalue</em> <br>
This keywords sets the initial time for molecular dynamics simulations
to <em>rvalue</em>. The default value is 0.000 ps.
<p>
<b><tt>Time step</tt></b> <em>rvalue</em> <br>
This keywords sets the time-step for molecular dynamics simulations
to <em>rvalue</em>. The default value is 0.001 ps.
<p>
<b><tt>SD iterations</tt></b> <em>ivalue</em> <br>
This keywords sets the maximum number of steepest descent iterations
for energy minimization calculations to <em>ivalue</em>.
The default value is 100.
<p>
<b><tt>SD initial step</tt></b> <em>rvalue</em> <br>
This keywords sets the initial step size for steepest descent
energy minimization calculations to <em>rvalue</em>.
The default value is 0.010 nm.
<p>
<b><tt>CG iterations</tt></b> <em>ivalue</em> <br>
This keywords sets the maximum number of conjugate gradient iterations
for energy minimization calculations to <em>ivalue</em>.
The default value is 0.
<p>
<b><tt>CG cycles</tt></b> <em>ivalue</em> <br>
This keywords sets the conjugate gradient refresh cycle
for energy minimization calculations to <em>ivalue</em>.
The default value is 0.
<p>
<b><tt>MCTI windows total</tt></b> <em>ivalue</em> <br>
This keywords sets the total number of multiconfiguration
thermodynamic integration steps for a free energy calculations
to <em>ivalue</em>. The default value is 21.
<p>
<b><tt>MCTI windows</tt></b> <em>ivalue</em> <br>
This keywords sets the number of multiconfiguration thermodynamic
integration steps for a free energy calculation that will be done
in this run to <em>ivalue</em>. The default value is equal to
the total number of integration steps.
<p>
<b><tt>MCTI separation shifted scaling delta</tt></b> <em>rvalue</em> <br>
This keywords sets the separation shifted scaling distance parameter
delta to <em>rvalue</em>. The default, and recommended, value is
0.075 nm^2.
<p>
<b><tt>MCTI separation shifted scaling</tt></b> <br>
This keyword activates separation shifted scaling in MCTI free
energy calculations. Per default separation shifted scaling is
turned off.
<p>
<b><tt>Print topology</tt></b> <br>
This keyword activates printing of the topology, for both solvent
and solute. Per default the topology is not printed.
<p>
<b><tt>Print topology solvent</tt></b> <br>
This keyword activates printing of the solvent topology.
Per default the solvent topology is not printed.
<p>
<b><tt>Print topology solute</tt></b> <br>
This keyword activates printing of the solute topology.
Per default the solute topology is not printed.
<p>
<b><tt>Print step</tt></b> <br>
This keyword activates printing of more detailed information
at each printed time step. Per default only total system energies
are printed.
<p>
<b><tt>Print step energies</tt></b> <br>
This keyword activates printing of even more detailed energy information
at each printed time step. Per default only total system energies
are printed.
<p>
<b><tt>Print timing analysis all nodes</tt></b> <br>
This keyword activates printing at the end of the run the timing
analysis of all nodes. Per default only the timing analysis
of node 0 is printed.
<p>
<b><tt>Equilibration steps</tt></b> <em>ivalue</em> <br>
This keyword sets the number of equilibration steps in an MD run
or in an MCTI window to <em>ivalue</em>. The default number
of equilibration steps is 0.
<p>
<b><tt>Data gathering steps</tt></b> <em>ivalue</em> <br>
This keyword sets the number of data gathering steps in an MD run
or in an MCTI window to <em>ivalue</em>. The default number
of data gathering steps is 100.
<p>
<b><tt>Cutoff radius WW SR</tt></b> <em>rvalue</em> <br>
<p>
<b><tt>Cutoff radius WW LR</tt></b> <em>rvalue</em> <br>
<p>
<b><tt>Cutoff radius SW SR</tt></b> <em>rvalue</em> <br>
<p>
<b><tt>Cutoff radius WS SR</tt></b> <em>rvalue</em> <br>
<p>
<b><tt>Cutoff radius SW LR</tt></b> <em>rvalue</em> <br>
<p>
<b><tt>Cutoff radius WS LR</tt></b> <em>rvalue</em> <br>
<p>
<b><tt>Cutoff radius SS SR</tt></b> <em>rvalue</em> <br>
<p>
<b><tt>Cutoff radius SS LR</tt></b> <em>rvalue</em> <br>
<p>
<b><tt>Cutoff radius SR</tt></b> <em>rvalue</em> <br>
This keyword sets all short-range cutoff radii to <em>rvalue</em>.
The default value is 0.9 nm.
<p>
<b><tt>Cutoff radius LR</tt></b> <em>rvalue</em> <br>
This keyword sets all long-range cutoff radii to <em>rvalue</em>.
The default value is 0.9 nm.
<p>
<b><tt>Cutoff radius</tt></b> <em>rvalue</em> <br>
This keyword sets all cutoff radii to <em>rvalue</em>.
The default value is 0.9 nm.
<p>
<b><tt>SHAKE iterations W</tt></b> <em>ivalue</em> <br>
This keywrods sets the maximum number of solvent SHAKE iterations
to <em>ivalue</em>. The default is 100.
<p>
<b><tt>SHAKE iterations S</tt></b> <em>ivalue</em> <br>
This keywrods sets the maximum number of solute SHAKE iterations
to <em>ivalue</em>. The default is 100.
<p>
<b><tt>SHAKE iterations</tt></b> <em>ivalue</em> <br>
This keywrods sets the maximum number of SHAKE iterations
to <em>ivalue</em> for both solvent and solute. The default is 100.
<p>
<b><tt>SHAKE tolerance W</tt></b> <em>rvalue</em> <br>
This keyword sets the solvent SHAKE tolerance to <em>rvalue</em>.
The default value is 0.001 nm.
<p>
<b><tt>SHAKE tolerance S</tt></b> <em>rvalue</em> <br>
This keyword sets the solute SHAKE tolerance to <em>rvalue</em>.
The default value is 0.001 nm.
<p>
<b><tt>SHAKE tolerance</tt></b> <em>rvalue</em> <br>
This keyword sets the SHAKE tolerance to <em>rvalue</em> for both
solvent and solute. The default value is 0.001 nm.
<p>
<b><tt>Binary recording</tt></b> <br>
This keyword enables binary recording. Per default all
recording files are ASCII formatted files.
<p>
<b><tt>Frequency centering solute</tt></b> <em>ivalue</em> <br>
This keyword sets the frequency of centering the solute center
of geometry. The default frequency is 0.
<p>
<b><tt>Frequency update pairlists</tt></b> <em>ivalue</em> <br>
This keyword sets the frequency of updating the pairlists.
The default frequency is 1.
<p>
<b><tt>Frequency update LR forces</tt></b> <em>ivalue</em> <br>
This keyword sets the frequency of updating the long range forces.
The default frequency is 1.
<p>
<b><tt>Frequency recording output</tt></b> <em>ivalue</em> <br>
This keyword sets the frequency of recording selected information
of a MD step, EM iteration or MCTI integration step to the output
file to <em>ivalue</em>. The default frequency is 1.
<p>
<b><tt>Frequency recording statistics</tt></b> <em>ivalue</em> <br>
This keyword sets the frequency of recording statistical information
accumulated during MD and MCTI calculations to output to <em>ivalue</em>.
The default frequency is 1.
<p>
<b><tt>Frequency recording restart</tt></b> <em>ivalue</em> <br>
This keyword sets the frequency of recording the restart file to
<em>ivalue</em>. The default value is 0.
<p>
<b><tt>Frequency recording free energy</tt></b> <em>ivalue</em> <br>
This keyword sets the frequency of recording the free energy data to
file to <em>ivalue</em>, during MCTI calculations. The default value
is 1.
<p>
<b><tt>Load balance box size</tt></b> <br>
This keyword specifies that loadbalancing is to be done based on
resizing of sub-boxes. Per default no load balancing is done.
<p>
<b><tt>Load balance box pairs</tt></b> <br>
This keyword specifies that loadbalancing is to be done based on
redistribution of internode sub-box pairs. Per default no load
balancing is done.
<p>
<b><tt>Constant pressure</tt></b> <em>rvalue</em> <br>
This keyword specifies that the simulation is to be done for a
constant pressure of <em>rvalue</em> Pa. Per default the simulation
is at constant volume.
<p>
<b><tt>Pressure relaxation time</tt></b> <em>rvalue</em> <br>
This keyword sets the pressure relation time to <em>rvalue</em> ps.
The default value is 0.5 ps.
<p>
<b><tt>Compressebility</tt></b> <em>rvalue</em> <br>
This keyword sets the compressebility of the molecular system
to <em>rvalue</em> ps. The default value is 4.53 10^10.
<p>
<b><tt>Constant temperature WS</tt></b> <em>rvalue</em> <br>
This keyword specifies that the simulation is to be done for a
constant temperature of <em>rvalue</em> K, in which the scaling
is done separately for solvent and solute. Per default the simulation
is at constant energy.
<p>
<b><tt>Constant temperature</tt></b> <em>rvalue</em> <br>
This keyword specifies that the simulation is to be done for a
constant temperature of <em>rvalue</em> K, in which the scaling
is done for the complete molecular system. Per default the simulation
is at constant energy.
<p>
<b><tt>Temperature relaxation time W</tt></b> <em>rvalue</em> <br>
This keyword sets the solvent temperature relation time to
<em>rvalue</em> ps. The default value is 0.1 ps.
<p>
<b><tt>Temperature relaxation time S</tt></b> <em>rvalue</em> <br>
This keyword sets the solute temperature relation time to
<em>rvalue</em> ps. The default value is 0.1 ps.
<p>
<b><tt>Temperature relaxation time</tt></b> <em>rvalue</em> <br>
This keyword sets the temperature relation time to
<em>rvalue</em> ps for both solvent and solute.
The default value is 0.1 ps.
<p>
<b><tt>Velocity reassignment frequency WS</tt></b> <em>ivalue</em> <br>
The keyword sets the velocity reassignment frequency to <em>ivalue</em>
for solvent and solute to separately obtain the reassigment
temperature. The default value is 0.
<p>
<b><tt>Velocity reassignment frequency</tt></b> <em>ivalue</em> <br>
The keyword sets the velocity reassignment frequency to <em>ivalue</em>
for the molecular system to obtain the reassigment temperature.
The default value is 0.
<p>
<b><tt>Velocity reassignment temperature</tt></b> <em>rvalue</em> <br>
This keyword sets the velocity reassignment temperature. The default
value is 298.15 K.
<p>
<hr>
</body>
</html>

18
doc/nwahtml/nwargos_intro.html Normal file
View file

@ -0,0 +1,18 @@
<html>
<title>nwARGOS introduction</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em><em>nwARGOS</em> introduction</em></h1>
<hr>
<p>
<em>nwArgos</em> is the <em>NWChem</em> module for molecular dynamics
simulations of macromolecules and solutions. The code is a parallel
implementation of <em>ARGOS</em>, a vectorized molecular dynamics
package developed by T.P.Straatsma at the University of Houston.
<p>
The <a href="nwargos_imple.html">parallel implementation</a> is based
on the spacial decomposition of the molecular system. This decomposition
makes the code especially efficient for large molecular systems.
<p>
<hr>
</body>
</html>

11
doc/nwahtml/nwargos_nwRST.html Normal file
View file

@ -0,0 +1,11 @@
<html>
<title>nwRST</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwRST</em></h1>
<hr>
<p>
<b><em>Restart generator</em></b>
<p>
<hr>
</body>
</html>

11
doc/nwahtml/nwargos_nwSGM.html Normal file
View file

@ -0,0 +1,11 @@
<html>
<title>nwSGM</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwSGM</em></h1>
<hr>
<p>
<b><em>Segment generator</em></b>
<p>
<hr>
</body>
</html>

42
doc/nwahtml/nwargos_nwTOP.html Normal file
View file

@ -0,0 +1,42 @@
<html>
<title>nwTOP</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1>Topology generator <em>nwTOP</em></h1>
<hr>
<p>
The <a href="nwargos_topology.html">topology</a> describes all static information
that describes a molecular system. This includes the connectivity, such
as bond-stretching, angle-bending and torsional interactions, as well as
non-bonded interactions, such as van der Waals and Coulombic interactions.
<p>
The <a href="nwargos_topology.html">topology</a> of a molecular system is
generated by the topology generator <em>nwTOP</em>. The molecular system
is described in terms of segments taken out of a database of predefined
segments. Segments that are not available in one of the database files
can be generated bye a utility program
<a href="nwargos_nwSGM.html">nwSGM</a>.
<p>
The command line to run <em>nwTOP</em> is
<p>
<tt>nwtop project forcefield</tt>
<p>
where <b>project</b> is the name of a sequence on one of the
sequence databases or a local file <b>project.seq</b>, and
<b>forcefield</b> is the name of one of the
<a href="nwargos_forcefields.html">available force fields</a>.
Force field parameters are taken from the parameter databases,
or from a local file <b>project.par</b> is present. The
<a href="nwargos_parameters.html"> format of the parameter
file</a> is identical to the <em>ARGOS</em> parameter file
format.
The resulting topology file is <b>project.top</b>
<p>
The input for <em>nwTOP</em> is taken from a sequence database, or
given in a formatted sequence file <b>project.seq</b>. A sequence
file may be appended to a sequence database. The
<a href="nwargos_sequence.html">format of a sequence
file</a> is slightly different from the <em>ARGOS</em> sequence file
format.
<hr>
</body>
</html>

26
doc/nwahtml/nwargos_nwinput.html Normal file
View file

@ -0,0 +1,26 @@
<html>
<title>NWChem input</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>NWChem input</em></h1>
<hr>
<p>
<b><em>NWChem input file format</em></b>
<p>
The input file for <em>NWChem</em> determines the module that will
be executed. For the <em>nwARGOS</em> module this file should be named
<b>project_id</b>. To run a molecular dynamics job using <em>nwARGOS</em>,
this file only the memory card, start and task card are required.
<p>
<hr>
An example of the input for <em>NWChem</em> is
<p>
<tt>
title; nwARGOS<br>
memory noverify heap 1 mb stack 32 mb global 8 mb<br>
start nwarg<br>
task nwargos<br>
</tt>
<p>
<hr>
</body>
</html>

28
doc/nwahtml/nwargos_restart.html Normal file
View file

@ -0,0 +1,28 @@
<html>
<title>nwArgos restart</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS restart</em></h1>
<hr>
<p>
All dynamic information of a molecular system needed to start or
restart a molecular simulation is provided in a restart file (<b>rst</b>).
This file contains, among other things, atomic coordinates and velocities,
accumulated properties and restraint information.
<br>
The initial restart file is generated by a utility
<a href="nwargos_nwRST.html"><b>nwRST</b></a>. This
program reads coordinates from an external source and writes a
restart file in the proper format for nwARGOS. The coordinates are
read from a <b>PDB</b> file, or from the <b>rst</b> file generated by
<a href="nwargos_nwRST.html"><b>nwRST</b></a> or <b>nwARGOS</b>. In addition,
<a href="nwargos_nwRST.html"><b>nwRST</b></a> performs
other operations, such as solvation, depending on information found
in a restart input file (<b>rin</b>).
<p>
<ul>
<li>Creating <b><em>rin</em></b> files
<li>Creating <b><em>rst</em></b> files
</ul>
</body>
</html>

105
doc/nwahtml/nwargos_sequence.html Normal file
View file

@ -0,0 +1,105 @@
<html>
<title>Sequence file format</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1>Sequence file format</h1>
<hr>
<table>
<tr>
<th>Card/Variable</th>
<th>Format</th>
<th>Description</th>
</tr>
<tr>
<td>I/1</td><td>A1</td><td><tt>$</tt> needed as search character</td>
</tr>
<tr>
<td>I/2</td><td>A10</td><td>Name of sequence</td>
</tr>
<tr>
<td>II/1</td><td>I5</td><td>Segment number, or<br> -1 to identify the
end of a molecule,<br> -2 to identify the end of the solute part of
the system,<br> -3 to identify the end of the sequence, or <br> 0 to
identify the solvent</td>
</tr>
<tr>
<td>II/2</td><td>A10</td><td>Segment name for 0 or positive segment
number<br>
</tr>
<tr>
<td>II/3</td><td>I5</td><td>First link segment number</td>
</tr>
<tr>
<td>II/4</td><td>I3</td><td>First link segment link atom</td>
</tr>
<tr>
<td>II/5</td><td>I5</td><td>Second link segment number</td>
</tr>
<tr>
<td>II/6</td><td>I3</td><td>Second link segment link atom</td>
</tr>
<tr>
<td>II/7</td><td>I5</td><td>Third link segment number</td>
</tr>
<tr>
<td>II/8</td><td>I3</td><td>Third link segment link atom</td>
</tr>
<tr>
<td>II/9</td><td>I5</td><td>Fourth link segment number</td>
</tr>
<tr>
<td>II/10</td><td>I3</td><td>Fourth link segment link atom</td>
</tr>
<tr>
<td>II/11</td><td>I5</td><td>Fifth link segment number</td>
</tr>
<tr>
<td>II/12</td><td>I3</td><td>Fifth link segment link atom</td>
</tr>
<tr>
<td>II/13</td><td>I5</td><td>Sixth link segment number</td>
</tr>
<tr>
<td>II/14</td><td>I3</td><td>Sixth link segment link atom</td>
</tr>
<tr>
<td>II/15</td><td>I5</td><td>Seventh link segment number</td>
</tr>
<tr>
<td>II/16</td><td>I3</td><td>Seventh link segment link atom</td>
</tr>
<tr>
<td>II/17</td><td>I5</td><td>Eighth link segment number</td>
</tr>
<tr>
<td>II/18</td><td>I3</td><td>Eighth link segment link atom</td>
</tr>
<tr>
<td>II/19</td><td>I5</td><td>Ninth link segment number</td>
</tr>
<tr>
<td>II/20</td><td>I3</td><td>Ninth link segment link atom</td>
</tr>
<tr>
<td>II/21</td><td>I5</td><td>Tenth link segment number</td>
</tr>
<tr>
<td>II/22</td><td>I3</td><td>Tenth link segment link atom</td>
</tr>
</table>
<p>
<b>Card I</b> needs a $ as the first character, immediately followed
by a 10 character identifying name for the system. These 11 characters
are used as a search string by <em>nwTOP</em>. Any number of lines
may preceed the first sequence card, for example to give a description
of the sequence and its author.<br>
<p>
<b>Card II</b> identifies an individual segment. Any number of Cards II
can be specified. If solvent is specified
it needs to be the last specified segment. If not given, first links are
made automatically to the segment on the previous card, unless its
segment number is negative. If not given, second links are made
automatically to the segment on the next card, unless its segment
number is negative.
<hr>
</body>
</html>

BIN
doc/nwahtml/nwargos_speedup_ksr2.gif Normal file
View file

Binary file not shown.
Side by side

After

Width:  |  Height:  |  Size: 17 KiB

BIN
doc/nwahtml/nwargos_speedup_sp2.gif Normal file
View file

Binary file not shown.
Side by side

After

Width:  |  Height:  |  Size: 13 KiB

48
doc/nwahtml/nwargos_topology.html Normal file
View file

@ -0,0 +1,48 @@
<html>
<title>nwArgos topology</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS topology</em></h1>
<hr>
<p>
The static information about a molecular system that is needed for
a molecular simulation is provided to the simulation module in a
topology file (<b>top</b>).
Items in this file include, among many other things,
a list of atoms, their non-bonded parameters for van der Waals and
electrostatic interactions, and a complete connectivity in terms
of bonds, angles and dihedrals.
<br>
In nwArgos, molecular systems are composed of <em>solvent</em> and
<em>solute</em>, which are treated separately. Solvent, is a collection
of identical molecules defined only once in the topology file. In the
current implementation only one solvent can be defined. Everything
else in the molecular system is solute. Solute is the collection of
molecules in the system of which each atom is explicitly defined in
the topology.
<br>
Molecular systems are defined in terms of <em>segment</em>s. Molecules
can be defined in a single segment, or as a collection of segments.
Typically, repetitive parts of a molecule are each defined as a single
segment. Segment files (<b>sgm</b>) can be quite complicated to define
and are, therefore, collected in a set of database libraries.
The list of segments and their connectivity that make a molecular system
is defined in a sequence file (<b>seq</b>).
A utility <b>nwTOP</b> reads the sequence from this file, retrieves all
needed segments from the available segment databases, and generates the
topology file.
<br>
Segments may not always be available in one of the existing databases.
A utility <b>nwSGM</b> reads a rudimentary, force-field independent
definition of a segment from a <em>fragment</em> file (<b>frg</b>), and
constructs a template for a force-field dependent segment.
Just like segments, fragments can be collected into a set of database files.
<p>
<ul>
<li>Creating <b><em>frg</em></b> files
<li>Creating <b><em>sgm</em></b> files
<li>Creating <b><em>seq</em></b> files
<li>Creating <b><em>top</em></b> files
</ul>
</body>
</html>

44
doc/nwahtml/nwargos_tutor.html Normal file
View file

@ -0,0 +1,44 @@
<html>
<title>nwArgos tutorial</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS tutorial</em></h1>
<hr>
<p>
Performing a simulation with <em>nwARGOS</em> requires a minimum of the following
four files. Following the conventions of the <a href="nwargos_files.html">
file structure</a>, these are
<ul>
<li><b>project.top</b>, describing the <a href="nwargos_topology.html">topology</a>
of the molecular system,
<li><b>project_id.rst</b>, constaining the <a href="nwargos_restart.html">(re-)start</a>
information,
<li><b>project_id.inp</b>, providing <a href="nwargos_input.html">input</a> details of
the simulation to <em>nwARGOS</em>, and
<li><b>project_id</b>, providing <a href="nwargos_nwinput.html">task</a> and memory
information to <em>NWChem</em>.
</ul>
<p>
Setting up a calculation is done in the following order
<ol>
<li>Create segment file <b>project.sgm</b>, using program
<a href="nwargos_nwSGM.html"><em>nwSGM</em></a>, if needed
<li>Create the topology file <b>project.top</b>, using program
<a href="nwargos_nwTOP.html"><em>nwTOP</em></a>
<li>Generate the restart file <b>project_id.rst</b>, using program
<a href="nwargos_nwRST.html"><em>nwRST</em></a>
<li>Provide in the input file <b>project_id.inp</b> a stream of
keywords defining the simulation details
<li>Provide in the <em>NWChem</em> input file <b>project_id</b>
the task and memory information
</ol>
<p>
The actual simulation is carried out with
<p>
<tt>nwchem project_id</tt>
<p>
<em>NWChem</em> will read the file <b>project_id</b>, allocate the specified memory and
give control to the <em>nwARGOS</em> module. <em>nwARGOS</em> will strip the <tt>project_id</tt>
from the command line, and generate all needed filenames, such as <b>project.top</b>,
<b>project_id.rst</b>, and <b>project_id.inp</b> from it.
</body>
</html>

16
doc/nwahtml/nwargos_xmpls.html Normal file
View file

@ -0,0 +1,16 @@
<html>
<title>nwArgos examples</title>
<body bgcolor="#000066" text="#FFFF00" link="#8888FF" vlink="#FF0000">
<h1><em>nwARGOS examples</em></h1>
<hr>
Example calculations available are
<p>
<a href="nwargos_ethanol,html"><b>etoh</b></a>: calculation of the absolute free
energy of hydration of ethanol.
<p>
<a href="nwargos_crown.html"><b>crown</b></a>: calculation of the free
energy difference between Na+ and K+ complexed in 18-crown-6.
<p>
<hr>
</body>
</html>