From 7237796f110179cef25aeed08de2f6e750d40503 Mon Sep 17 00:00:00 2001 From: Tjerk Straatsma Date: Wed, 26 Jun 1996 23:05:32 +0000 Subject: [PATCH] HTML files describing nwargos --- doc/nwahtml/nwargos.files.html | 9 + doc/nwahtml/nwargos.html | 24 + doc/nwahtml/nwargos_bmrks.html | 44 ++ doc/nwahtml/nwargos_bmrks_bucket.html | 159 ++++++ doc/nwahtml/nwargos_bmrks_drop.html | 158 ++++++ doc/nwahtml/nwargos_bmrks_ocean.html | 123 +++++ doc/nwahtml/nwargos_bmrks_river.html | 135 +++++ doc/nwahtml/nwargos_bmrks_sea.html | 138 +++++ doc/nwahtml/nwargos_bmrks_water_ksr.html | 9 + doc/nwahtml/nwargos_bmrks_water_sp2.html | 9 + doc/nwahtml/nwargos_crown.html | 63 +++ doc/nwahtml/nwargos_crown_frg.html | 27 + doc/nwahtml/nwargos_crown_seq.html | 29 + doc/nwahtml/nwargos_crown_sgm.html | 62 +++ doc/nwahtml/nwargos_crown_top.html | 665 +++++++++++++++++++++++ doc/nwahtml/nwargos_extensions.html | 83 +++ doc/nwahtml/nwargos_files.html | 65 +++ doc/nwahtml/nwargos_forcefields.html | 35 ++ doc/nwahtml/nwargos_funct.html | 9 + doc/nwahtml/nwargos_imple.html | 9 + doc/nwahtml/nwargos_input.html | 325 +++++++++++ doc/nwahtml/nwargos_intro.html | 18 + doc/nwahtml/nwargos_nwRST.html | 11 + doc/nwahtml/nwargos_nwSGM.html | 11 + doc/nwahtml/nwargos_nwTOP.html | 42 ++ doc/nwahtml/nwargos_nwinput.html | 26 + doc/nwahtml/nwargos_restart.html | 28 + doc/nwahtml/nwargos_sequence.html | 105 ++++ doc/nwahtml/nwargos_speedup_ksr2.gif | Bin 0 -> 17328 bytes doc/nwahtml/nwargos_speedup_sp2.gif | Bin 0 -> 13620 bytes doc/nwahtml/nwargos_topology.html | 48 ++ doc/nwahtml/nwargos_tutor.html | 44 ++ doc/nwahtml/nwargos_xmpls.html | 16 + 33 files changed, 2529 insertions(+) create mode 100644 doc/nwahtml/nwargos.files.html create mode 100644 doc/nwahtml/nwargos.html create mode 100644 doc/nwahtml/nwargos_bmrks.html create mode 100644 doc/nwahtml/nwargos_bmrks_bucket.html create mode 100644 doc/nwahtml/nwargos_bmrks_drop.html create mode 100644 doc/nwahtml/nwargos_bmrks_ocean.html create mode 100644 doc/nwahtml/nwargos_bmrks_river.html create mode 100644 doc/nwahtml/nwargos_bmrks_sea.html create mode 100644 doc/nwahtml/nwargos_bmrks_water_ksr.html create mode 100644 doc/nwahtml/nwargos_bmrks_water_sp2.html create mode 100644 doc/nwahtml/nwargos_crown.html create mode 100644 doc/nwahtml/nwargos_crown_frg.html create mode 100644 doc/nwahtml/nwargos_crown_seq.html create mode 100644 doc/nwahtml/nwargos_crown_sgm.html create mode 100644 doc/nwahtml/nwargos_crown_top.html create mode 100644 doc/nwahtml/nwargos_extensions.html create mode 100644 doc/nwahtml/nwargos_files.html create mode 100644 doc/nwahtml/nwargos_forcefields.html create mode 100644 doc/nwahtml/nwargos_funct.html create mode 100644 doc/nwahtml/nwargos_imple.html create mode 100644 doc/nwahtml/nwargos_input.html create mode 100644 doc/nwahtml/nwargos_intro.html create mode 100644 doc/nwahtml/nwargos_nwRST.html create mode 100644 doc/nwahtml/nwargos_nwSGM.html create mode 100644 doc/nwahtml/nwargos_nwTOP.html create mode 100644 doc/nwahtml/nwargos_nwinput.html create mode 100644 doc/nwahtml/nwargos_restart.html create mode 100644 doc/nwahtml/nwargos_sequence.html create mode 100644 doc/nwahtml/nwargos_speedup_ksr2.gif create mode 100644 doc/nwahtml/nwargos_speedup_sp2.gif create mode 100644 doc/nwahtml/nwargos_topology.html create mode 100644 doc/nwahtml/nwargos_tutor.html create mode 100644 doc/nwahtml/nwargos_xmpls.html diff --git a/doc/nwahtml/nwargos.files.html b/doc/nwahtml/nwargos.files.html new file mode 100644 index 0000000000..1ba7d3ecd4 --- /dev/null +++ b/doc/nwahtml/nwargos.files.html @@ -0,0 +1,9 @@ + +nwArgos file structure + +

nwARGOS molecular dynamics simulations file structure

+
+

+File structure + + diff --git a/doc/nwahtml/nwargos.html b/doc/nwahtml/nwargos.html new file mode 100644 index 0000000000..449c67c966 --- /dev/null +++ b/doc/nwahtml/nwargos.html @@ -0,0 +1,24 @@ + + +nwArgos molecular dynamics simulations + + +

nwARGOS molecular dynamics simulations

+
+nwARGOS is the module in NWChem for molecular dynamics simulations of +macromolecular, liquid, and solution systems. This document provides a +description for this module. +

+

+

+

+ + diff --git a/doc/nwahtml/nwargos_bmrks.html b/doc/nwahtml/nwargos_bmrks.html new file mode 100644 index 0000000000..77c8910a98 --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks.html @@ -0,0 +1,44 @@ + +nwArgos benchmarks + +

nwARGOS benchmarks

+
+

SPC/E water

+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. +

+drop: a molecular dynamics simulation of 216 SPC/E water molecules +

+bucket: a molecular dynamics simulation of 1,728 SPC/E water molecules +

+river: a molecular dynamics simulation of 5,832 SPC/E water molecules +

+sea: a molecular dynamics simulation of 13,824 SPC/E water molecules +

+ocean: a molecular dynamics simulation of 27,000 SPC/E water molecules +

+

+

Myoglobin

+

+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. +

+myo: a molecular dynamics simulation of myoglobin in SPC/E water (10,914 atoms) +

+

+
+

Speedup curves

+

+For selected benchmarks speedup curves are compared as obtained for the +KSR-2 and the +IBM SP-2. +

+

+ + + diff --git a/doc/nwahtml/nwargos_bmrks_bucket.html b/doc/nwahtml/nwargos_bmrks_bucket.html new file mode 100644 index 0000000000..25cb679ac9 --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks_bucket.html @@ -0,0 +1,159 @@ + +nwArgos bucket benchmark + +

nwARGOS bucket benchmark

+
+

Molecular dynamics simulation of 1,728 SPC/E water molecules

+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. +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
KSR-2IBM SP-2
+4 nodes + +1.695529 + + +
+8 nodes + +0.835476 + + +
+16 nodes + +0.448117 + + +
+32 nodes + +0.275099 + + +
+64 nodes + +0.203467 + + +
+

+Speedups relative to the 4 node timings + +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
KSR-2IBM SP-2
+4 nodes + +4.0 + + +
+8 nodes + +8.1 + + +
+16 nodes + +15.1 + + +
+32 nodes + +24.7 + + +
+64 nodes + +33.3 + + +
+

+

+ + + diff --git a/doc/nwahtml/nwargos_bmrks_drop.html b/doc/nwahtml/nwargos_bmrks_drop.html new file mode 100644 index 0000000000..9d266560b1 --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks_drop.html @@ -0,0 +1,158 @@ + +nwArgos drop benchmark + +

nwARGOS drop benchmark

+
+

Molecular dynamics simulation of 216 SPC/E water molecules

+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. +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
KSR-2IBM SP-2
+4 nodes + +0.294088 + + +
+8 nodes + +0.165577 + + +
+16 nodes + +0.101206 + + +
+32 nodes + +0.110004 + + +
+64 nodes + +0.181529 + + +
+

+Speedups relative to the 4 node timings + +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
KSR-2IBM SP-2
+4 nodes + +4.0 + + +
+8 nodes + +7.1 + + +
+16 nodes + +11.6 + + +
+32 nodes + +10.7 + + +
+64 nodes + +6.5 + + +
+

+

+ + diff --git a/doc/nwahtml/nwargos_bmrks_ocean.html b/doc/nwahtml/nwargos_bmrks_ocean.html new file mode 100644 index 0000000000..ac2a709e1e --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks_ocean.html @@ -0,0 +1,123 @@ + +nwArgos ocean benchmark + +

nwARGOS ocean benchmark

+
+

Molecular dynamics simulation of 27,000 SPC/E water molecules

+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. +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
KSR-2IBM SP-2
Rc=0.9Rc=0.9
4 nodes15.035754
8 nodes7.290162
20 nodes2.717282
32 nodes2.766097
50 nodes1.472683
125 nodes1.107691
+

+Speedups relative to the 4 node timings + +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
KSR-2IBM SP-2
Rc=0.9Rc=0.9
4 nodes4.0
8 nodes8.3
20 nodes22.1
32 nodes21.7
50 nodes40.8
125 nodes54.3
+

+

+ + + diff --git a/doc/nwahtml/nwargos_bmrks_river.html b/doc/nwahtml/nwargos_bmrks_river.html new file mode 100644 index 0000000000..d6f7978841 --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks_river.html @@ -0,0 +1,135 @@ + +nwArgos river benchmark + +

nwARGOS river benchmark

+
+

Molecular dynamics simulation of 5,832 SPC/E water molecules

+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. +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
KSR-2IBM SP-2
+4 nodes + +6.118019 + +3.023760 +
+8 nodes + +2.866662 + +1.664759 +
+27 nodes + +0.889270 + + +
+72 nodes + +0.408092 + + +
+

+Speedups relative to the 4 node timings + +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
KSR-2IBM SP-2
+4 nodes + +4.0 + +4.0 +
+8 nodes + +8.5 + +7.3 +
+27 nodes + +27.5 + + +
+72 nodes + +60.0 + + +
+

+

+ + + diff --git a/doc/nwahtml/nwargos_bmrks_sea.html b/doc/nwahtml/nwargos_bmrks_sea.html new file mode 100644 index 0000000000..ed09846ba1 --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks_sea.html @@ -0,0 +1,138 @@ + +nwArgos sea benchmark + +

nwARGOS sea benchmark

+
+

Molecular dynamics simulation of 13,824 SPC/E water molecules

+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. +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
KSR-2IBM SP-2IBM SP-2
Rc=0.9Rc=0.9Rc=1.8
4 nodes15.1179767.33196952.237927
8 nodes7.1691063.81624427.631083
16 nodes3.4724682.13073513.496562
32 nodes1.7821876.811522
64 nodes0.9213441.0076763.663068
128 nodes2.280681
+

+Speedups relative to the 4 node timings + +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
KSR-2IBM SP-2
Rc=0.9Rc=0.9Rc=1.8
4 nodes4.04.04.0
8 nodes8.58.07.6
16 nodes17.414.515.5
32 nodes33.925.936.0
64 nodes65.630.157.1
128 nodes91.6
+

+

+ + + diff --git a/doc/nwahtml/nwargos_bmrks_water_ksr.html b/doc/nwahtml/nwargos_bmrks_water_ksr.html new file mode 100644 index 0000000000..688eca5f4b --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks_water_ksr.html @@ -0,0 +1,9 @@ + +nwArgos KSR-2 benchmarks + +

nwARGOS KSR-2 benchmarks

+
+ +
+ + diff --git a/doc/nwahtml/nwargos_bmrks_water_sp2.html b/doc/nwahtml/nwargos_bmrks_water_sp2.html new file mode 100644 index 0000000000..d7572c5141 --- /dev/null +++ b/doc/nwahtml/nwargos_bmrks_water_sp2.html @@ -0,0 +1,9 @@ + +nwArgos IBM SP-2 benchmarks + +

nwARGOS IBM SP-2 benchmarks

+
+ +
+ + diff --git a/doc/nwahtml/nwargos_crown.html b/doc/nwahtml/nwargos_crown.html new file mode 100644 index 0000000000..9bf72be0ad --- /dev/null +++ b/doc/nwahtml/nwargos_crown.html @@ -0,0 +1,63 @@ + +nwArgos example: crown + +

nwARGOS example: crown

+
+

+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. +

+

    +
  1. +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 +coc_______.frg. +

    +

  2. +The fragment just created is force field independent. To create the +force field amber dependent segment file, give the command +

    +nwsgm coc_______ amber +

    +This command searches the fragment libraries and the local file +coc_______.frg for a fragment entry $coc. +The generic atom types defined in the fragment are substituted for +the amber atom types. The translation tables are found in +the atom type translation library files or the local file +coc_______.att, if present. +A segment file coc_______.sgm +is created that should be renamed to crown.sgm. +Alternatively, this file may be appended to +amber_u.sgm or amber_r.sgm, provided that these library +files are defined in the file $HOME/.nwargos. +

    +

  3. +A sequence file needs to be created, defining the molecular system +in terms of segments. Using an editor create the file +crown.seq. This file defines +the 18C6 crown ether in terms of six cyclicly arranged coc +fragments. It also specifies the solvent as the SPC/E water model. +

    +

  4. +The topology file crown.top is +created, giving the command +

    +nwtop crown amber +

    +This command searches the amber sequence database files, and +the local sequence file crown.seq for a sequence crown. +The force field needs to be given in order to search the correct +database files. If the sequence is found, it searches the amber +segment databases and the local segment file crown.sgm 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 amber parameter library files, and the local file +crown.par if present. Any segments or parameters not found +can be supplied in the local files. +

+ + diff --git a/doc/nwahtml/nwargos_crown_frg.html b/doc/nwahtml/nwargos_crown_frg.html new file mode 100644 index 0000000000..f3e64a308f --- /dev/null +++ b/doc/nwahtml/nwargos_crown_frg.html @@ -0,0 +1,27 @@ + +nwArgos example: crown: coc fragment file + +

nwARGOS example: crown: coc fragment file

+
+

+

+$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
+
+

+

+Note that the first atom (C1) is defined as first link +atom, and the fifth atom (C2) is defined as second link +atom. + + diff --git a/doc/nwahtml/nwargos_crown_seq.html b/doc/nwahtml/nwargos_crown_seq.html new file mode 100644 index 0000000000..0d475fed2e --- /dev/null +++ b/doc/nwahtml/nwargos_crown_seq.html @@ -0,0 +1,29 @@ + +nwArgos example: crown: sequence file + +

nwARGOS example: crown: sequence file

+
+

+

+$crown 
+    1coc
+    2coc
+    3coc
+    4coc
+    5coc
+    6coc           0  0    1  1
+   -2
+    0SPCE
+   -3
+
+

+

+Note that the sixth coc segment's second link is pointing +to the first link atom of the first coc segment, to make +the cyclic crown ether. Alternatively this could have been specified +by letting the first coc segment's first link point to the +sixth coc segment's second link atom. The other coc +segments are automatically link their first link atom to their previous +segment's second link atom. + + diff --git a/doc/nwahtml/nwargos_crown_sgm.html b/doc/nwahtml/nwargos_crown_sgm.html new file mode 100644 index 0000000000..dd7d328b33 --- /dev/null +++ b/doc/nwahtml/nwargos_crown_sgm.html @@ -0,0 +1,62 @@ + +nwArgos example: crown: coc fragment file + +

nwARGOS example: crown: coc fragment file

+
+

+

+$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
+
+

+

+ + diff --git a/doc/nwahtml/nwargos_crown_top.html b/doc/nwahtml/nwargos_crown_top.html new file mode 100644 index 0000000000..d153aae2aa --- /dev/null +++ b/doc/nwahtml/nwargos_crown_top.html @@ -0,0 +1,665 @@ + +nwArgos example: crown: topology file + +

nwARGOS example: crown: topology file

+
+

+

+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
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+      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
+
+
+

+

+ + diff --git a/doc/nwahtml/nwargos_extensions.html b/doc/nwahtml/nwargos_extensions.html new file mode 100644 index 0000000000..54f93704fa --- /dev/null +++ b/doc/nwahtml/nwargos_extensions.html @@ -0,0 +1,83 @@ + +nwArgos extensions + +

nwARGOS extensions

+
+

+File extensions +

+The following file extensions are used by nwARGOS and the setup +programs nwTOP, +nwRST and +nwSGM. +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ExtensionFile description
coo coordinate file
inp input file
prp property file
rin nwRST input file
rou nwRST output file
rst restart file
seq nwTOP sequence input file
sco solute coordinate file
svl solute velocity file
top topology file
vel velocity file
+

+

+Database extensions +

+The following file extensions are used by the setup programs +nwTOP, +nwRST and +nwSGM. +

+ + + + + + + + + + + + + + + + + + + + +
ExtensionFile description
att atom type database
frg fragment database
par parameter database
sgm segment database
slv solvent restart file
+ + diff --git a/doc/nwahtml/nwargos_files.html b/doc/nwahtml/nwargos_files.html new file mode 100644 index 0000000000..0f71c267b3 --- /dev/null +++ b/doc/nwahtml/nwargos_files.html @@ -0,0 +1,65 @@ + +nwArgos file structure + +

nwARGOS file structure

+
+

+File names +

+File names used by nwARGOS need to have the form +project_id.ext, with exception of the +topology file, which should be named project.top, and the input +file for NWChem, which should simply be project. +Anything that refers to the definition of the chemical system can be used +for project, as long as no periods or underlines are used.
+The identifier id can be anything that refers to the type of calculation +to be performed for the system.
+The extensions ext +identify the kind of information on the file, and are determined by the +programs. Examples of extensions are top for the topology file, +rst for the restart file and inp for the input file. +

+This file naming convention allows for the creation of a single topology file +project.top for a chemical system with which a number of different +calculations, identified with different id. +

+

+

+Database names +

+A similar convention is used to identify databases used by the setup programs +nwTOP, +nwRST and +nwSGM. +Force field database names have the form +forcefield_level.ext, where forcefield stands for any of the +supported force fields. The source +of the data is identified by level, and can be +

+ + + + + + + + + + + + + + + + +
levelDescriptionAvailability
soriginal published datapublic
xadditional published datapublic
uuser preferred dataprivate
ruser defined run specific dataprivate
+

+Only the level s and x databases are publicly available. The user is +responsible for the private level u and r databases. +

+Other database files include the force field independent fragment libraries and +the solvation restart files. +

+

+ + diff --git a/doc/nwahtml/nwargos_forcefields.html b/doc/nwahtml/nwargos_forcefields.html new file mode 100644 index 0000000000..0824c7a02e --- /dev/null +++ b/doc/nwahtml/nwargos_forcefields.html @@ -0,0 +1,35 @@ + +nwArgos force fields + +

nwARGOS supported force fields

+
+

+Force fields supported by nwARGOS are +

+ + + + + + + + + + + + + + + + + + + + + + +
KeywordForce field nameCurrent status
amber AMBER4.0available
charmm CHARMMplanned
cvff CVFFplanned
gromos GROMOS87planned
oplsa OPLS/AMBER3.0planned
oplsg OPLS/GROMOS87planned
+

+

+ + diff --git a/doc/nwahtml/nwargos_funct.html b/doc/nwahtml/nwargos_funct.html new file mode 100644 index 0000000000..29dac384d7 --- /dev/null +++ b/doc/nwahtml/nwargos_funct.html @@ -0,0 +1,9 @@ + +nwArgos functionality + +

nwARGOS molecular dynamics simulations functionality

+
+

+Functionality + + diff --git a/doc/nwahtml/nwargos_imple.html b/doc/nwahtml/nwargos_imple.html new file mode 100644 index 0000000000..262de8c04b --- /dev/null +++ b/doc/nwahtml/nwargos_imple.html @@ -0,0 +1,9 @@ + +nwArgos parallel implementation + +

nwARGOS molecular dynamics simulations parallel implementation

+
+

+Parallel implementation + + diff --git a/doc/nwahtml/nwargos_input.html b/doc/nwahtml/nwargos_input.html new file mode 100644 index 0000000000..83eec75f4f --- /dev/null +++ b/doc/nwahtml/nwargos_input.html @@ -0,0 +1,325 @@ + +nwArgos input + +

nwARGOS input

+
+

+Input file format +

+The input file project_id.inp determines the type of calculation +to be performed. Details of the calculation are given in keyworded +format. +

+Input file keywords +

+Keywords need to be given exactly as given below. Numeric values are +in free format. Keywords recognized include +

+#
+Any card in the input file that starts with the number sign (#) is +treated as a comment, and ignored. +

+
+Any card in the input file that starts with a space is +treated as a comment, and ignored. +

+Title
+Three title cards (a) and one with date and time (2a10) are read. +

+Task SP
+Identifies that a single point energy evaluation is to be done using +parameters from set 1. +This card cancels any previous Task cards in the input +deck. +

+Task SP set 2
+Identifies that a single point energy evaluation is to be done using +parameters from set 2. +This card cancels any previous Task cards in the input +deck. +

+Task SP set 3
+Identifies that a single point energy evaluation is to be done using +parameters from set 3. +This card cancels any previous Task cards in the input +deck. +

+Task MD
+Identifies that a molecular dynamics simulation is to be carried out using +parameters from set 1. +This card cancels any previous Task cards in the input +deck. +

+Task MD set 2
+Identifies that a molecular dynamics simulation is to be carried out using +parameters from set 2. +This card cancels any previous Task cards in the input +deck. +

+Task MD set 3
+Identifies that a molecular dynamics simulation is to be carried out using +parameters from set 3. +This card cancels any previous Task cards in the input +deck. +

+Task EM
+Identifies that an energy minimization is to be performed out using +parameters from set 1. +This card cancels any previous Task cards in the input +deck. +

+Task EM set 2
+Identifies that an energy minimization is to be performed out using +parameters from set 2. +This card cancels any previous Task cards in the input +deck. +

+Task EM set 3
+Identifies that an energy minimization is to be performed out using +parameters from set 3. +This card cancels any previous Task cards in the input +deck. +

+Task MCTI
+Identifies that a multiconfiguration thermodynamic integration +calculation will be carried out. +This card cancels any previous Task cards in the input +deck. +

+Start time rvalue
+This keywords sets the initial time for molecular dynamics simulations +to rvalue. The default value is 0.000 ps. +

+Time step rvalue
+This keywords sets the time-step for molecular dynamics simulations +to rvalue. The default value is 0.001 ps. +

+SD iterations ivalue
+This keywords sets the maximum number of steepest descent iterations +for energy minimization calculations to ivalue. +The default value is 100. +

+SD initial step rvalue
+This keywords sets the initial step size for steepest descent +energy minimization calculations to rvalue. +The default value is 0.010 nm. +

+CG iterations ivalue
+This keywords sets the maximum number of conjugate gradient iterations +for energy minimization calculations to ivalue. +The default value is 0. +

+CG cycles ivalue
+This keywords sets the conjugate gradient refresh cycle +for energy minimization calculations to ivalue. +The default value is 0. +

+MCTI windows total ivalue
+This keywords sets the total number of multiconfiguration +thermodynamic integration steps for a free energy calculations +to ivalue. The default value is 21. +

+MCTI windows ivalue
+This keywords sets the number of multiconfiguration thermodynamic +integration steps for a free energy calculation that will be done +in this run to ivalue. The default value is equal to +the total number of integration steps. +

+MCTI separation shifted scaling delta rvalue
+This keywords sets the separation shifted scaling distance parameter +delta to rvalue. The default, and recommended, value is +0.075 nm^2. +

+MCTI separation shifted scaling
+This keyword activates separation shifted scaling in MCTI free +energy calculations. Per default separation shifted scaling is +turned off. +

+Print topology
+This keyword activates printing of the topology, for both solvent +and solute. Per default the topology is not printed. +

+Print topology solvent
+This keyword activates printing of the solvent topology. +Per default the solvent topology is not printed. +

+Print topology solute
+This keyword activates printing of the solute topology. +Per default the solute topology is not printed. +

+Print step
+This keyword activates printing of more detailed information +at each printed time step. Per default only total system energies +are printed. +

+Print step energies
+This keyword activates printing of even more detailed energy information +at each printed time step. Per default only total system energies +are printed. +

+Print timing analysis all nodes
+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. +

+Equilibration steps ivalue
+This keyword sets the number of equilibration steps in an MD run +or in an MCTI window to ivalue. The default number +of equilibration steps is 0. +

+Data gathering steps ivalue
+This keyword sets the number of data gathering steps in an MD run +or in an MCTI window to ivalue. The default number +of data gathering steps is 100. +

+Cutoff radius WW SR rvalue
+

+Cutoff radius WW LR rvalue
+

+Cutoff radius SW SR rvalue
+

+Cutoff radius WS SR rvalue
+

+Cutoff radius SW LR rvalue
+

+Cutoff radius WS LR rvalue
+

+Cutoff radius SS SR rvalue
+

+Cutoff radius SS LR rvalue
+

+Cutoff radius SR rvalue
+This keyword sets all short-range cutoff radii to rvalue. +The default value is 0.9 nm. +

+Cutoff radius LR rvalue
+This keyword sets all long-range cutoff radii to rvalue. +The default value is 0.9 nm. +

+Cutoff radius rvalue
+This keyword sets all cutoff radii to rvalue. +The default value is 0.9 nm. +

+SHAKE iterations W ivalue
+This keywrods sets the maximum number of solvent SHAKE iterations +to ivalue. The default is 100. +

+SHAKE iterations S ivalue
+This keywrods sets the maximum number of solute SHAKE iterations +to ivalue. The default is 100. +

+SHAKE iterations ivalue
+This keywrods sets the maximum number of SHAKE iterations +to ivalue for both solvent and solute. The default is 100. +

+SHAKE tolerance W rvalue
+This keyword sets the solvent SHAKE tolerance to rvalue. +The default value is 0.001 nm. +

+SHAKE tolerance S rvalue
+This keyword sets the solute SHAKE tolerance to rvalue. +The default value is 0.001 nm. +

+SHAKE tolerance rvalue
+This keyword sets the SHAKE tolerance to rvalue for both +solvent and solute. The default value is 0.001 nm. +

+Binary recording
+This keyword enables binary recording. Per default all +recording files are ASCII formatted files. +

+Frequency centering solute ivalue
+This keyword sets the frequency of centering the solute center +of geometry. The default frequency is 0. +

+Frequency update pairlists ivalue
+This keyword sets the frequency of updating the pairlists. +The default frequency is 1. +

+Frequency update LR forces ivalue
+This keyword sets the frequency of updating the long range forces. +The default frequency is 1. +

+Frequency recording output ivalue
+This keyword sets the frequency of recording selected information +of a MD step, EM iteration or MCTI integration step to the output +file to ivalue. The default frequency is 1. +

+Frequency recording statistics ivalue
+This keyword sets the frequency of recording statistical information +accumulated during MD and MCTI calculations to output to ivalue. +The default frequency is 1. +

+Frequency recording restart ivalue
+This keyword sets the frequency of recording the restart file to +ivalue. The default value is 0. +

+Frequency recording free energy ivalue
+This keyword sets the frequency of recording the free energy data to +file to ivalue, during MCTI calculations. The default value +is 1. +

+Load balance box size
+This keyword specifies that loadbalancing is to be done based on +resizing of sub-boxes. Per default no load balancing is done. +

+Load balance box pairs
+This keyword specifies that loadbalancing is to be done based on +redistribution of internode sub-box pairs. Per default no load +balancing is done. +

+Constant pressure rvalue
+This keyword specifies that the simulation is to be done for a +constant pressure of rvalue Pa. Per default the simulation +is at constant volume. +

+Pressure relaxation time rvalue
+This keyword sets the pressure relation time to rvalue ps. +The default value is 0.5 ps. +

+Compressebility rvalue
+This keyword sets the compressebility of the molecular system +to rvalue ps. The default value is 4.53 10^10. +

+Constant temperature WS rvalue
+This keyword specifies that the simulation is to be done for a +constant temperature of rvalue K, in which the scaling +is done separately for solvent and solute. Per default the simulation +is at constant energy. +

+Constant temperature rvalue
+This keyword specifies that the simulation is to be done for a +constant temperature of rvalue K, in which the scaling +is done for the complete molecular system. Per default the simulation +is at constant energy. +

+Temperature relaxation time W rvalue
+This keyword sets the solvent temperature relation time to +rvalue ps. The default value is 0.1 ps. +

+Temperature relaxation time S rvalue
+This keyword sets the solute temperature relation time to +rvalue ps. The default value is 0.1 ps. +

+Temperature relaxation time rvalue
+This keyword sets the temperature relation time to +rvalue ps for both solvent and solute. +The default value is 0.1 ps. +

+Velocity reassignment frequency WS ivalue
+The keyword sets the velocity reassignment frequency to ivalue +for solvent and solute to separately obtain the reassigment +temperature. The default value is 0. +

+Velocity reassignment frequency ivalue
+The keyword sets the velocity reassignment frequency to ivalue +for the molecular system to obtain the reassigment temperature. +The default value is 0. +

+Velocity reassignment temperature rvalue
+This keyword sets the velocity reassignment temperature. The default +value is 298.15 K. +

+

+ + diff --git a/doc/nwahtml/nwargos_intro.html b/doc/nwahtml/nwargos_intro.html new file mode 100644 index 0000000000..8c30a93ab4 --- /dev/null +++ b/doc/nwahtml/nwargos_intro.html @@ -0,0 +1,18 @@ + +nwARGOS introduction + +

nwARGOS introduction

+
+

+nwArgos is the NWChem module for molecular dynamics +simulations of macromolecules and solutions. The code is a parallel +implementation of ARGOS, a vectorized molecular dynamics +package developed by T.P.Straatsma at the University of Houston. +

+The parallel implementation is based +on the spacial decomposition of the molecular system. This decomposition +makes the code especially efficient for large molecular systems. +

+

+ + diff --git a/doc/nwahtml/nwargos_nwRST.html b/doc/nwahtml/nwargos_nwRST.html new file mode 100644 index 0000000000..16a8987c8b --- /dev/null +++ b/doc/nwahtml/nwargos_nwRST.html @@ -0,0 +1,11 @@ + +nwRST + +

nwRST

+
+

+Restart generator +

+

+ + diff --git a/doc/nwahtml/nwargos_nwSGM.html b/doc/nwahtml/nwargos_nwSGM.html new file mode 100644 index 0000000000..e2bba39adc --- /dev/null +++ b/doc/nwahtml/nwargos_nwSGM.html @@ -0,0 +1,11 @@ + +nwSGM + +

nwSGM

+
+

+Segment generator +

+

+ + diff --git a/doc/nwahtml/nwargos_nwTOP.html b/doc/nwahtml/nwargos_nwTOP.html new file mode 100644 index 0000000000..0757d952b8 --- /dev/null +++ b/doc/nwahtml/nwargos_nwTOP.html @@ -0,0 +1,42 @@ + +nwTOP + +

Topology generator nwTOP

+
+

+The topology 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. +

+The topology of a molecular system is +generated by the topology generator nwTOP. 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 +nwSGM. +

+The command line to run nwTOP is +

+nwtop project forcefield +

+where project is the name of a sequence on one of the +sequence databases or a local file project.seq, and +forcefield is the name of one of the +available force fields. +Force field parameters are taken from the parameter databases, +or from a local file project.par is present. The + format of the parameter +file is identical to the ARGOS parameter file +format. +The resulting topology file is project.top +

+The input for nwTOP is taken from a sequence database, or +given in a formatted sequence file project.seq. A sequence +file may be appended to a sequence database. The +format of a sequence +file is slightly different from the ARGOS sequence file +format. +

+ + diff --git a/doc/nwahtml/nwargos_nwinput.html b/doc/nwahtml/nwargos_nwinput.html new file mode 100644 index 0000000000..2dffafa82f --- /dev/null +++ b/doc/nwahtml/nwargos_nwinput.html @@ -0,0 +1,26 @@ + +NWChem input + +

NWChem input

+
+

+NWChem input file format +

+The input file for NWChem determines the module that will +be executed. For the nwARGOS module this file should be named +project_id. To run a molecular dynamics job using nwARGOS, +this file only the memory card, start and task card are required. +

+

+An example of the input for NWChem is +

+ +title; nwARGOS
+memory noverify heap 1 mb stack 32 mb global 8 mb
+start nwarg
+task nwargos
+ +

+

+ + diff --git a/doc/nwahtml/nwargos_restart.html b/doc/nwahtml/nwargos_restart.html new file mode 100644 index 0000000000..7269b4746f --- /dev/null +++ b/doc/nwahtml/nwargos_restart.html @@ -0,0 +1,28 @@ + +nwArgos restart + +

nwARGOS restart

+
+

+All dynamic information of a molecular system needed to start or +restart a molecular simulation is provided in a restart file (rst). +This file contains, among other things, atomic coordinates and velocities, +accumulated properties and restraint information. +
+The initial restart file is generated by a utility +nwRST. 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 PDB file, or from the rst file generated by +nwRST or nwARGOS. In addition, +nwRST performs +other operations, such as solvation, depending on information found +in a restart input file (rin). +

+

+ + + diff --git a/doc/nwahtml/nwargos_sequence.html b/doc/nwahtml/nwargos_sequence.html new file mode 100644 index 0000000000..cd5448077b --- /dev/null +++ b/doc/nwahtml/nwargos_sequence.html @@ -0,0 +1,105 @@ + +Sequence file format + +

Sequence file format

+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Card/VariableFormatDescription
I/1A1$ needed as search character
I/2A10Name of sequence
II/1I5Segment number, or
-1 to identify the +end of a molecule,
-2 to identify the end of the solute part of +the system,
-3 to identify the end of the sequence, or
0 to +identify the solvent
II/2A10Segment name for 0 or positive segment +number
+
II/3I5First link segment number
II/4I3First link segment link atom
II/5I5Second link segment number
II/6I3Second link segment link atom
II/7I5Third link segment number
II/8I3Third link segment link atom
II/9I5Fourth link segment number
II/10I3Fourth link segment link atom
II/11I5Fifth link segment number
II/12I3Fifth link segment link atom
II/13I5Sixth link segment number
II/14I3Sixth link segment link atom
II/15I5Seventh link segment number
II/16I3Seventh link segment link atom
II/17I5Eighth link segment number
II/18I3Eighth link segment link atom
II/19I5Ninth link segment number
II/20I3Ninth link segment link atom
II/21I5Tenth link segment number
II/22I3Tenth link segment link atom
+

+Card I 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 nwTOP. Any number of lines +may preceed the first sequence card, for example to give a description +of the sequence and its author.
+

+Card II 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. +

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nwARGOS topology

+
+

+The static information about a molecular system that is needed for +a molecular simulation is provided to the simulation module in a +topology file (top). +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. +
+In nwArgos, molecular systems are composed of solvent and +solute, 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. +
+Molecular systems are defined in terms of segments. 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 (sgm) 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 (seq). +A utility nwTOP reads the sequence from this file, retrieves all +needed segments from the available segment databases, and generates the +topology file. +
+Segments may not always be available in one of the existing databases. +A utility nwSGM reads a rudimentary, force-field independent +definition of a segment from a fragment file (frg), and +constructs a template for a force-field dependent segment. +Just like segments, fragments can be collected into a set of database files. +

+

    +
  • Creating frg files +
  • Creating sgm files +
  • Creating seq files +
  • Creating top files +
+ + + diff --git a/doc/nwahtml/nwargos_tutor.html b/doc/nwahtml/nwargos_tutor.html new file mode 100644 index 0000000000..31e66003f0 --- /dev/null +++ b/doc/nwahtml/nwargos_tutor.html @@ -0,0 +1,44 @@ + +nwArgos tutorial + +

nwARGOS tutorial

+
+

+Performing a simulation with nwARGOS requires a minimum of the following +four files. Following the conventions of the +file structure, these are +

    +
  • project.top, describing the topology + of the molecular system, +
  • project_id.rst, constaining the (re-)start + information, +
  • project_id.inp, providing input details of + the simulation to nwARGOS, and +
  • project_id, providing task and memory + information to NWChem. +
+

+Setting up a calculation is done in the following order +

    +
  1. Create segment file project.sgm, using program + nwSGM, if needed +
  2. Create the topology file project.top, using program + nwTOP +
  3. Generate the restart file project_id.rst, using program + nwRST +
  4. Provide in the input file project_id.inp a stream of + keywords defining the simulation details +
  5. Provide in the NWChem input file project_id + the task and memory information +
+

+The actual simulation is carried out with +

+nwchem project_id +

+NWChem will read the file project_id, allocate the specified memory and +give control to the nwARGOS module. nwARGOS will strip the project_id +from the command line, and generate all needed filenames, such as project.top, +project_id.rst, and project_id.inp from it. + + diff --git a/doc/nwahtml/nwargos_xmpls.html b/doc/nwahtml/nwargos_xmpls.html new file mode 100644 index 0000000000..756eb106a0 --- /dev/null +++ b/doc/nwahtml/nwargos_xmpls.html @@ -0,0 +1,16 @@ + +nwArgos examples + +

nwARGOS examples

+
+Example calculations available are +

+etoh: calculation of the absolute free +energy of hydration of ethanol. +

+crown: calculation of the free +energy difference between Na+ and K+ complexed in 18-crown-6. +

+

+ +