mirror of
https://github.com/nwchemgit/nwchem.git
synced 2026-07-27 13:45:27 -04:00
1094 lines
36 KiB
HTML
1094 lines
36 KiB
HTML
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
|
|
|
|
<!--Converted with jLaTeX2HTML 2002 (1.62) JA patch-1.4
|
|
patched version by: Kenshi Muto, Debian Project.
|
|
LaTeX2HTML 2002 (1.62),
|
|
original version by: Nikos Drakos, CBLU, University of Leeds
|
|
* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
|
|
* with significant contributions from:
|
|
Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
|
|
<HTML>
|
|
<HEAD>
|
|
<TITLE>30. Prepare</TITLE>
|
|
<META NAME="description" CONTENT="30. Prepare">
|
|
<META NAME="keywords" CONTENT="user">
|
|
<META NAME="resource-type" CONTENT="document">
|
|
<META NAME="distribution" CONTENT="global">
|
|
|
|
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
|
|
<META NAME="Generator" CONTENT="jLaTeX2HTML v2002 JA patch-1.4">
|
|
<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
|
|
|
|
<LINK REL="STYLESHEET" HREF="user.css">
|
|
|
|
<LINK REL="next" HREF="node33.html">
|
|
<LINK REL="previous" HREF="node31.html">
|
|
<LINK REL="up" HREF="user.html">
|
|
<LINK REL="next" HREF="node33.html">
|
|
</HEAD>
|
|
|
|
<BODY BGCOLOR="#FFFFFF">
|
|
<!--Navigation Panel-->
|
|
<A NAME="tex2html1585"
|
|
HREF="node33.html">
|
|
<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="next.png"></A>
|
|
<A NAME="tex2html1581"
|
|
HREF="user.html">
|
|
<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up.png"></A>
|
|
<A NAME="tex2html1575"
|
|
HREF="node31.html">
|
|
<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="prev.png"></A>
|
|
<A NAME="tex2html1583"
|
|
HREF="node2.html">
|
|
<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="contents.png"></A>
|
|
<BR>
|
|
<B> Next:</B> <A NAME="tex2html1586"
|
|
HREF="node33.html">31. Molecular dynamics</A>
|
|
<B> Up:</B> <A NAME="tex2html1582"
|
|
HREF="user.html">user</A>
|
|
<B> Previous:</B> <A NAME="tex2html1576"
|
|
HREF="node31.html">29. Electrostatic potentials</A>
|
|
  <B> <A NAME="tex2html1584"
|
|
HREF="node2.html">Contents</A></B>
|
|
<BR>
|
|
<BR>
|
|
<!--End of Navigation Panel-->
|
|
<!--Table of Child-Links-->
|
|
<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
|
|
|
|
<UL>
|
|
<LI><A NAME="tex2html1587"
|
|
HREF="node32.html#SECTION003210000000000000000">30.1 Default database directories</A>
|
|
<LI><A NAME="tex2html1588"
|
|
HREF="node32.html#SECTION003220000000000000000">30.2 System name and coordinate source</A>
|
|
<LI><A NAME="tex2html1589"
|
|
HREF="node32.html#SECTION003230000000000000000">30.3 Sequence file generation</A>
|
|
<LI><A NAME="tex2html1590"
|
|
HREF="node32.html#SECTION003240000000000000000">30.4 Topology file generation</A>
|
|
<LI><A NAME="tex2html1591"
|
|
HREF="node32.html#SECTION003250000000000000000">30.5 Appending to an existing topology file</A>
|
|
<LI><A NAME="tex2html1592"
|
|
HREF="node32.html#SECTION003260000000000000000">30.6 Generating a restart file</A>
|
|
</UL>
|
|
<!--End of Table of Child-Links-->
|
|
<HR>
|
|
|
|
<H1><A NAME="SECTION003200000000000000000">
|
|
30. Prepare</A>
|
|
</H1>
|
|
<A NAME="sec:prepare"></A>
|
|
|
|
<P>
|
|
The <B>prepare</B> module is used to set up the necessary files for a molecular
|
|
dynamics simulation with <B>NWChem</B>. User supplied coordinates can be used to
|
|
generate topology and restart files. The topology file contains all static
|
|
information about a molecular system, such as lists of atoms, bonded
|
|
interactions and force field parameters. The restart file contains all
|
|
dynamic information about a molecular system, such as coordinates, velocities
|
|
and properties.
|
|
|
|
<P>
|
|
Without any input, the prepare module checks the existence of a topology
|
|
and restart file for the molecular systems. If these files exist, the module
|
|
returns to the main task level without action. The module will generate these
|
|
files when they do not exist. Without any input to the module, the generated
|
|
system will be for a non-solvated isolated solute system.
|
|
|
|
<P>
|
|
To update existing files, including solvation, the module requires input
|
|
directives read from an input deck,
|
|
|
|
<P>
|
|
<PRE>
|
|
prepare
|
|
...
|
|
end
|
|
</PRE>
|
|
|
|
<P>
|
|
The prepare module performs three sub-tasks:
|
|
<DL COMPACT>
|
|
<DT><B>*</B></DT>
|
|
<DD><B>sequence generation</B>
|
|
<BR>
|
|
This sub-task analyzes the supplied coordinates from a PDB-formatted file
|
|
or from the input geometry, and generates a sequence file, containing the
|
|
description of the system in terms of basic building blocks found as
|
|
fragment or segment files in the database directories for the force field
|
|
used. If these files do not exist, they are generated based on the supplied
|
|
coordinates. This process constists of generating a fragment file with the
|
|
list of atoms with their force field dependent atom types, partial atomic
|
|
charges calculated from a Hartree Fock calculation for the fragment, followed
|
|
by a restrained electrostatic potential fit, and a connectivity list. From
|
|
the information on this fragment file the lists of all bonded interactions
|
|
are generated, and the complete lists are written to a segment file.
|
|
</DD>
|
|
<DT><B>*</B></DT>
|
|
<DD><B>topology generation</B>
|
|
<BR>
|
|
Based on the generated or user-supplied sequence file and the force field
|
|
specific segment database files, this sub-task compiles the lists of atoms,
|
|
bonded interactions, excluded pairs, and substitutes the force field
|
|
parameters. Special commands may be given to specify interaction parameters
|
|
that will be changing in a free energy evaluation.
|
|
</DD>
|
|
<DT><B>*</B></DT>
|
|
<DD><B>restart generation</B>
|
|
<BR>
|
|
Using the user supplied coordinates and the topology file for the chemical
|
|
system, this sub-task generates a restart file for the system with coordinates,
|
|
velocities and other dynamic information. This step may include solvation
|
|
of the chemical system and specifying periodic boundary conditions.
|
|
</DD>
|
|
</DL>
|
|
|
|
<P>
|
|
Files involved in the preparation phase exist in the following hierarchy:
|
|
<DL COMPACT>
|
|
<DT><B>*</B></DT>
|
|
<DD><B>standards</B>
|
|
<BR>
|
|
The standard database files contain the original force field information.
|
|
These files are to reside in a directory that is specified in the file
|
|
$HOME/.nwchemrc. There will be such a directory for each supported force
|
|
field. These directories contain fragment files (with extension frg),
|
|
segment files (with extension sgm) and a parameter file (with the name
|
|
of the force field and with extension par).
|
|
</DD>
|
|
<DT><B>*</B></DT>
|
|
<DD><B>extensions</B>
|
|
<BR>
|
|
These database files contain generally accepted extensions to the original
|
|
force field and are to reside in a separate directory that is specified in
|
|
the file $HOME/.nwchemrc. There will be such a directory for each supported
|
|
force field. These directories contain fragment files (with extension frg),
|
|
segment files (with extension sgm) and a parameter file (with the name
|
|
of the force field and with extension par).
|
|
</DD>
|
|
<DT><B>*</B></DT>
|
|
<DD><B>contributed</B>
|
|
<BR>
|
|
These database files contain contributed definitions, also required for
|
|
the quality assurance tests and are to reside in a separate directory
|
|
that is specified in the file $HOME/.nwchemrc.
|
|
There will be such a directory for each supported
|
|
force field. These directories contain fragment files (with extension frg),
|
|
segment files (with extension sgm) and a parameter file (with the name
|
|
of the force field and with extension par).
|
|
</DD>
|
|
<DT><B>*</B></DT>
|
|
<DD><B>user preferences</B>
|
|
<BR>
|
|
These database files contain user preferred extensions to the original
|
|
force field and are to reside in a separate directory that is specified in
|
|
the file $HOME/.nwchemrc. Separate directories of this type should be
|
|
defined for each supported force field.
|
|
This directory may contain fragment files (with extension frg),
|
|
segment files (with extension sgm) and a parameter file (with the name
|
|
of the force field and with extension par).
|
|
</DD>
|
|
<DT><B>*</B></DT>
|
|
<DD><B>temporary files</B>
|
|
<BR>
|
|
Temporary database files contain user preferred extensions to the original
|
|
force field and are to reside in a separate directory that is specified in
|
|
the file $HOME/.nwchemrc. There may be such a directory for each supported
|
|
force field. This directory may contain fragment files (with extension frg),
|
|
segment files (with extension sgm) and a parameter file (with the name
|
|
of the force field and with extension par).
|
|
</DD>
|
|
<DT><B>*</B></DT>
|
|
<DD><B>current files</B>
|
|
<BR>
|
|
Database files that contain user preferred extensions to the original
|
|
force field and are to reside in a separate directory that is specified in
|
|
the file $HOME/.nwchemrc. Typically this will be the current working
|
|
directory, although it may be defined as a specific directory.
|
|
This directory may contain fragment files (with extension frg),
|
|
segment files (with extension sgm) and a parameter file (with the name
|
|
of the force field and with extension par). If not specified,
|
|
files will be taken from the current directory.
|
|
</DD>
|
|
</DL>
|
|
|
|
<P>
|
|
Data is taken from the database files searched in the above order. If data
|
|
is specified more than once, the last found values are used. For example,
|
|
if some standard segment is redefined in a temporary file, the latter one
|
|
will be used. This allows the user to redefine standards or extensions
|
|
without having to modify those database files, which may reside in a
|
|
generally available, non-modifyable directory. If a filename is specified
|
|
rather than a directory, the filename indicates the parameter file
|
|
definition. All other files (frg and sgm files) will be take from the
|
|
specified directory.
|
|
|
|
<P>
|
|
The most common problems with the <B>prepare</B> module are
|
|
<DL COMPACT>
|
|
<DT><B> </B></DT>
|
|
<DD>The format of the pdb file does not conform to the pdb standard. In
|
|
particular, atom names need to correspond with definitions in the
|
|
fragment and segment database files, and should adhere to IUPAC
|
|
recommendations as adopted by the pdb standard. If this problem
|
|
occurs, the pdb file will need to be corrected.
|
|
</DD>
|
|
<DT><B> </B></DT>
|
|
<DD>Non-standard segments may contain atoms that could not be atom typed
|
|
with the existing typing rules in the force field parameter files.
|
|
When this happens, additional typing rules can be included in the
|
|
parameter file, or the fragment file may be manually typed.
|
|
</DD>
|
|
<DT><B> </B></DT>
|
|
<DD>Parameters for atom types or bonded interactions do not exist in
|
|
the force field. When this happens, additional parameters may be
|
|
defined in the parameter files, or the segment file may be edited
|
|
to include explicit parameters.
|
|
</DD>
|
|
</DL>
|
|
|
|
<P>
|
|
|
|
<H1><A NAME="SECTION003210000000000000000">
|
|
30.1 Default database directories</A>
|
|
</H1>
|
|
|
|
<P>
|
|
The file $HOME/.nwchemrc may contain the following entries that determine
|
|
which files are used by the prepare module.
|
|
|
|
<P>
|
|
<PRE>
|
|
ffield <string ffname>
|
|
</PRE>
|
|
|
|
<P>
|
|
This entry specifies the default force field. Database files supplied with
|
|
<B>NWChem</B> currently support values for <code>ffname</code> of <B>amber</B>, referring
|
|
to AMBER95, and <B>charmm</B>, referring to the academic CHARMM22 force field.
|
|
|
|
<P>
|
|
<PRE>
|
|
<string ffname>_(s | x | q | u | t | c) <string ffdir>[<string parfile>]
|
|
</PRE>
|
|
|
|
<P>
|
|
Entries of this type specify the directory <code>ffdir</code> in which force field
|
|
database files can be found. Optionally the parameterfile in this directory
|
|
may be specified as <code>parfile</code>.
|
|
The prepare module will only use files in directories
|
|
specified here. One exception is that files in the current work directory
|
|
will be used if no directory with current files is specified.
|
|
|
|
<P>
|
|
<PRE>
|
|
<string solvnam> <string solvfil>
|
|
</PRE>
|
|
|
|
<P>
|
|
This entry may be used to identify a pure solvent restart file <code>solvfil</code>
|
|
by a name <code>solvnam</code>
|
|
|
|
<P>
|
|
An example file $HOME/.nwchemrc is:
|
|
|
|
<P>
|
|
<PRE>
|
|
ffield amber
|
|
amber_s /msrc/proj/nwchem/share/amber/amber_s/amber99.par
|
|
amber_x /msrc/proj/nwchem/share/amber/amber_x/
|
|
amber_u /usr/people/username/data/amber/amber_u/
|
|
spce /msrc/proj/nwchem/share/solvents/spce.rst
|
|
charmm_s /msrc/proj/nwchem/share/charmm/charmm_s/
|
|
charmm_x /msrc/proj/nwchem/share/charmm/charmm_x/
|
|
</PRE>
|
|
|
|
<P>
|
|
|
|
<H1><A NAME="SECTION003220000000000000000">
|
|
30.2 System name and coordinate source</A>
|
|
</H1>
|
|
|
|
<P>
|
|
<PRE>
|
|
system <string sys_calc>
|
|
</PRE>
|
|
|
|
<P>
|
|
The system name can be explicitly specified for the <B>prepare</B> module.
|
|
If not specified, the system name will be taken from a specification
|
|
in a previous <B>md</B> input block, or derived from the run time database
|
|
name.
|
|
|
|
<P>
|
|
<PRE>
|
|
source ( pdb | rtdb )
|
|
</PRE>
|
|
|
|
<P>
|
|
The source of the coordinates can be explicitly specified to be from
|
|
a PDB formatted file <code>sys</code>.pdb, or from a geometry object in the run
|
|
time database. If not specified, a pdb file will be used when it exists
|
|
in the current directory or the rtdb geometry otherwise.
|
|
|
|
<P>
|
|
<PRE>
|
|
model <integer modpdb default 0>
|
|
</PRE>
|
|
|
|
<P>
|
|
If a PDB formatted source file contains different MODELs, the <code>model</code>
|
|
keyword can be used to specify which MODEL will be used to generate the
|
|
topology and restart file. If not specified, the first MODEL found on the
|
|
PDB file will be read.
|
|
|
|
<P>
|
|
<PRE>
|
|
altloc <character locpdb default ' '>
|
|
</PRE>
|
|
|
|
<P>
|
|
The <code>altloc</code> keyword may be used to specify the use of alternate
|
|
location coordinates on a PDB file.
|
|
|
|
<P>
|
|
<PRE>
|
|
chain <character chnpdb default ' '>
|
|
</PRE>
|
|
|
|
<P>
|
|
The <code>chain</code> keyword may be used to specify the chain identifier
|
|
for coordinates on a PDB file.
|
|
|
|
<P>
|
|
<PRE>
|
|
histidine ( hid | hie | hip )
|
|
</PRE>
|
|
specifies the default protonation state of histidine.
|
|
|
|
<P>
|
|
<PRE>
|
|
sscyx
|
|
</PRE>
|
|
|
|
<P>
|
|
Keyword <code>sscyx</code> may be used to rename cysteine residues that form
|
|
sulphur bridges to CYX.
|
|
|
|
<P>
|
|
<PRE>
|
|
hbuild
|
|
</PRE>
|
|
|
|
<P>
|
|
Keyword <code>hbuild</code> may be used to add hydrogen atoms to the
|
|
unknown segments of the structure found on the pdb file.
|
|
|
|
<P>
|
|
|
|
<H1><A NAME="SECTION003230000000000000000">
|
|
30.3 Sequence file generation</A>
|
|
</H1>
|
|
|
|
<P>
|
|
If no existing sequence file is present in the current directory,
|
|
or if the <code>new_seq</code> keyword was specified in the <B>prepare</B>
|
|
input deck, a new sequence file is generated from information
|
|
from the pdb file, and the following input directives.
|
|
|
|
<P>
|
|
<PRE>
|
|
maxscf <integer maxscf default 20>
|
|
</PRE>
|
|
|
|
<P>
|
|
Variable maxscf specifies the maximum number of atoms in a segment for
|
|
which partial atomic charges will be determined from an SCF calculation
|
|
followed by RESP charge fitting. For larger segments a crude partial
|
|
charge guestimation will be done.
|
|
|
|
<P>
|
|
<PRE>
|
|
qscale <real qscale default 1.0>
|
|
</PRE>
|
|
|
|
<P>
|
|
Variable qscale specifies the factor with which SCF/RESP determined
|
|
charges will be multiplied.
|
|
|
|
<P>
|
|
<PRE>
|
|
modify sequence { <integer sgmnum>:<string sgmnam> }
|
|
</PRE>
|
|
|
|
<P>
|
|
This command specifies that segment <B>sgmnam</B> should be used
|
|
for segment with number <I>sgmnum</I>. This command can be used
|
|
to specify a particular protonation state. For example, the
|
|
following command specifies that residue 114 is a hystidine
|
|
protonated at the N<IMG
|
|
WIDTH="10" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img200.gif"
|
|
ALT="$_\epsilon$"> site and residue 202 is a hystidine
|
|
protonated at the N<IMG
|
|
WIDTH="11" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img201.gif"
|
|
ALT="$_\delta$"> site:
|
|
|
|
<P>
|
|
<PRE>
|
|
modify sequence 114:HIE 202:HID
|
|
</PRE>
|
|
|
|
<P>
|
|
Links between atoms can be enforced with
|
|
|
|
<P>
|
|
<PRE>
|
|
link <string atomname> <string atomname>
|
|
</PRE>
|
|
|
|
<P>
|
|
For example, to link atom SG in segment 20 with atom FE
|
|
in segment 55, use:
|
|
|
|
<P>
|
|
<PRE>
|
|
link 20:_SG 55:FE
|
|
</PRE>
|
|
|
|
<P>
|
|
The format of the sequence file is given in Table <A HREF="node36.html#tbl:nwmdseq">34.8</A>.
|
|
In addition to the list of segments this file also includes links
|
|
between non-standard segments or other non-standard links.
|
|
These links are generated based on distances found between
|
|
atoms on the pdb file. When atoms are involved in such non-standard
|
|
links that have not been identified in the fragment of segment
|
|
files as a non-chain link atom, the prepare module will ignore
|
|
these links and report them as skipped. If one or more of these links
|
|
are required, the user has to include them with explicit link
|
|
directives in the sequence file, making them forced links.
|
|
Alternatively, these links can be made forced-links by changing
|
|
<code>link</code> into <code>LINK</code> in the sequence file.
|
|
|
|
<P>
|
|
<PRE>
|
|
fraction { <integer imol> }
|
|
</PRE>
|
|
|
|
<P>
|
|
Directive <code>fraction</code> can be used to separate solute molecules
|
|
into fractions for which energies will be separately reported
|
|
during molecular dynamics simulations. The listed molecules will be
|
|
the last molecule in a fraction. Up to 10 molecules may be
|
|
specified in this directive.
|
|
|
|
<P>
|
|
<PRE>
|
|
counter <integer num> <string ion>
|
|
</PRE>
|
|
|
|
<P>
|
|
Directive <code>counter</code> adds <code>num</code> counter ions of type
|
|
<code>ion</code> to the sequence file. Up to 10 <code>counter</code>
|
|
directives may appear in the input block.
|
|
|
|
<P>
|
|
<PRE>
|
|
counter <real factor>
|
|
</PRE>
|
|
|
|
<P>
|
|
This directive scales the counter ion charge by the specified factor
|
|
in the determination of counter ions positions.
|
|
|
|
<P>
|
|
|
|
<H1><A NAME="SECTION003240000000000000000">
|
|
30.4 Topology file generation</A>
|
|
</H1>
|
|
|
|
<P>
|
|
<PRE>
|
|
new_top [ new_seq ]
|
|
</PRE>
|
|
|
|
<P>
|
|
Keyword <code>new_top</code> is used to force the generation of a new topology
|
|
file. An existing topology file for the system in the current directory
|
|
will be overwritten. If keyword <code>new_seq</code> is also specified, an
|
|
existing sequence file will also be overwritten with a newly generated
|
|
file.
|
|
|
|
<P>
|
|
<PRE>
|
|
amber | charmm
|
|
</PRE>
|
|
|
|
<P>
|
|
The prepare module generates force field specific fragment, segment and
|
|
topology files. The force field may be explicitly specified in the prepare
|
|
input block by specifying its name.
|
|
Currently <B>AMBER</B> and <B>CHARMM</B> are the supported force fields.
|
|
A default force field may be specified in the file $HOME/.nwchemrc.
|
|
|
|
<P>
|
|
<PRE>
|
|
standard <string dir_s>[<string par_s>]
|
|
extensions <string dir_x>[<string par_x>]
|
|
contributed <string dir_q>[<string par_q>]
|
|
user <string dir_u>[<string par_u>]
|
|
temporary <string dir_t>[<string par_t>]
|
|
current <string dir_c>[<string par_c>]
|
|
</PRE>
|
|
|
|
<P>
|
|
The user can explicitly specify the directories where force field
|
|
specific databases can be found. These include force field standards,
|
|
extensions, quality assurance tests, user preferences, temporary , and
|
|
current database files.
|
|
<BR>
|
|
Defaults for the directories where database files reside may be specified
|
|
in the file $HOME/.nwchemrc for each of the supported force fields.
|
|
Fragment, segment and sequence files generated by the <B>prepare</B> module are
|
|
written in the temporary directory. When not specified, the current
|
|
directory will be used.
|
|
Topology and restart files are always created in the current directory.
|
|
|
|
<P>
|
|
The following directives control the modifications of a
|
|
topology file. These directives are executed in the order in which
|
|
they appear in the <B>prepare</B> input deck. The topology modifying
|
|
commands are not stored on the run-time database and are, therefor,
|
|
not persistent.
|
|
|
|
<P>
|
|
<PRE>
|
|
modify atom <string atomname> [set <integer mset> | initial | final] \
|
|
( type <string atomtyp> | charge <real atomcharge> | \
|
|
polar <real atompolar> | dummy | self | quantum | quantum_high )
|
|
</PRE>
|
|
|
|
<P>
|
|
These <code>modify</code> commands change the atom type, partial atomic charge,
|
|
atomic polarizability, specify a dummy, self-interaction and quantum atom,
|
|
respectively. If <code>mset</code> is specified, the modification will only
|
|
apply to the specified set, which has to be 1, 2 or 3. If not specified,
|
|
the modification will be applied to all three sets. The quantum region in
|
|
QM/MM simulations is defined by specifying atoms with the <code>quantum</code>
|
|
or <code>quantum_high</code> label. For atoms defined <code>quantum_high</code>
|
|
basis sets labeled <code>X_H</code> will be used.
|
|
The <code>atomnam</code>
|
|
should be specified as <code><integer isgm>:<string name></code>, where
|
|
<code>isgm</code> is the segment number, and <code>name</code> is the atom name. A
|
|
leading blank in an atom name should be substituted with an underscore.
|
|
The modify commands may be combined. For example, the following directive
|
|
changes for the specified atom the charge and atom type in set 2 and
|
|
specifies the atom to be a dummy in set 3.
|
|
|
|
<P>
|
|
<PRE>
|
|
modify atom 12:_C1 set 2 charge 0.12 type CA set 3 dummy
|
|
</PRE>
|
|
|
|
<P>
|
|
With the following directives modifications can be made for entire
|
|
segments.
|
|
|
|
<P>
|
|
<PRE>
|
|
modify segment <integer isgm> [set <integer mset> | initial | final] \
|
|
( dummy | self | uncharged | quantum | quantum_high )
|
|
</PRE>
|
|
|
|
<P>
|
|
Modifications to bonded interaction parameters can be made with the
|
|
following modify commands.
|
|
|
|
<P>
|
|
<PRE>
|
|
modify ( bond <string atomtyp> <string atomtyp> | \
|
|
angle <string atomtyp> <string atomtyp> <string atomtyp> | \
|
|
torsion <string atomtyp> <string atomtyp> <string atomtyp> \
|
|
<string atomtyp> [ multiplicity <integer multip> ] | \
|
|
plane <string atomtyp> <string atomtyp> <string atomtyp> \
|
|
<string atomtyp> ) [set <integer mset> | initial | final] \
|
|
<real value> <real forcon>
|
|
</PRE>
|
|
|
|
<P>
|
|
where <code>atomtyp</code> and <code>mset</code> are defined as above, <code>multip</code>
|
|
is the torsion ultiplicity for which the modification is to be applied,
|
|
<code>value</code> is the reference bond, angle, torsion angle of out-of-plane
|
|
angle value respectively, and <code>forcon</code> is the force constant for
|
|
bond, angle, torsion angle of out-of-plane angle. When <code>multip</code>
|
|
or <code>mset</code> are not defined the modification will be applied to
|
|
all multiplicities and sets, respectively, for the identified bonded
|
|
interaction.
|
|
|
|
<P>
|
|
After modifying atoms to quantum atoms the bonded interactions in which
|
|
only quantum atoms are involved are removed from the bonded lists using
|
|
|
|
<P>
|
|
<PRE>
|
|
update lists
|
|
</PRE>
|
|
|
|
<P>
|
|
Error messages resulting from parameters not being defined for bonded
|
|
interaction in which only quantum atoms are involved are ignored using
|
|
|
|
<P>
|
|
<PRE>
|
|
ignore
|
|
</PRE>
|
|
|
|
<P>
|
|
|
|
<H1><A NAME="SECTION003250000000000000000">
|
|
30.5 Appending to an existing topology file</A>
|
|
</H1>
|
|
|
|
<P>
|
|
<PRE>
|
|
noe <string atom1> <string atom3> \
|
|
<real dist1> <real dist2> <real dist3> <real forc1> <real forc2>
|
|
</PRE>
|
|
|
|
<P>
|
|
This directive specifies a distance restraint potential between atoms
|
|
<IMG
|
|
WIDTH="48" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img202.gif"
|
|
ALT="$atom1$"> and <IMG
|
|
WIDTH="48" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img203.gif"
|
|
ALT="$atom2$">, with a harmonic function with force constant
|
|
<IMG
|
|
WIDTH="44" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img204.gif"
|
|
ALT="$forc1$"> between <IMG
|
|
WIDTH="39" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img205.gif"
|
|
ALT="$dist1$"> and <IMG
|
|
WIDTH="39" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img206.gif"
|
|
ALT="$dist2$">, and a harmonic function with
|
|
force constant <IMG
|
|
WIDTH="44" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
|
|
SRC="img207.gif"
|
|
ALT="$forc2$"> between <IMG
|
|
WIDTH="39" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img206.gif"
|
|
ALT="$dist2$"> and <IMG
|
|
WIDTH="39" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img208.gif"
|
|
ALT="$dist3$">. For distances
|
|
shorter than <IMG
|
|
WIDTH="39" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img205.gif"
|
|
ALT="$dist1$"> or larger than <IMG
|
|
WIDTH="39" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img208.gif"
|
|
ALT="$dist3$">, a constant force is
|
|
applied such that force and energy are continuous at <IMG
|
|
WIDTH="39" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img205.gif"
|
|
ALT="$dist1$">
|
|
and <IMG
|
|
WIDTH="39" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img208.gif"
|
|
ALT="$dist3$">, respectively. Distances are given in nm, force constants
|
|
in kJ mol<IMG
|
|
WIDTH="21" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img209.gif"
|
|
ALT="$^{-1}$"> nm<IMG
|
|
WIDTH="21" HEIGHT="17" ALIGN="BOTTOM" BORDER="0"
|
|
SRC="img210.gif"
|
|
ALT="$^{-2}$">.
|
|
|
|
<P>
|
|
<PRE>
|
|
select <integer isel> { <string atoms> }
|
|
</PRE>
|
|
|
|
<P>
|
|
Directive <code>select</code> specifies a group of atoms used in the
|
|
definition of potential of mean force potentials.
|
|
|
|
<P>
|
|
The selected atoms are specified by the string <code>atoms</code> which
|
|
takes the form
|
|
|
|
<P>
|
|
<PRE>
|
|
[{isgm [ - jsgm ] [,]} [:] [{aname[,]}]
|
|
</PRE>
|
|
|
|
<P>
|
|
For example, all carbon and oxygen atoms in segments 3
|
|
and 6 through 12 are selected for group 1 by
|
|
|
|
<P>
|
|
<PRE>
|
|
3,6-12:_C????,_O????
|
|
</PRE>
|
|
|
|
<P>
|
|
<PRE>
|
|
pmf [all] [bias] zalign <integer isel> <real forcon1> <real forcon2>
|
|
pmf [combine] [bias] xyplane <integer isel> <real forcon1> <real forcon2>
|
|
pmf [constraint] [bias] (distance | zdistance) <integer isel> <integer jsel> \
|
|
<real dist1> <real dist2> <real forcon1> <real forcon2>
|
|
pmf [bias] angle <integer isel> <integer jsel> <integer ksel> \
|
|
<real angle1> <real angle2> <real forcon1> <real forcon2>
|
|
pmf [bias] torsion <integer isel> <integer jsel> <integer ksel> <integer lsel> \
|
|
<real angle1> <real angle2> <real forcon1> <real forcon2>
|
|
pmf [bias] basepair <integer isel> <integer jsel> \
|
|
<real dist1> <real dist2> <real forcon1> <real forcon2>
|
|
pmf [bias] (zaxis | zaxis-cog) <integer isel> <integer jsel> <integer ksel> \
|
|
<real dist1> <real dist2> <real forcon1> <real forcon2>
|
|
</PRE>
|
|
|
|
<P>
|
|
Directive <code>pmf</code> specifies a potential of mean force potential
|
|
in terms of the specified atom selection. Option <code>zalign</code> specifies
|
|
the atoms in the selection to be restrained to a line parallel to the
|
|
z-axis. Option <code>xyplane</code> specifies the atoms in the selection to
|
|
be restrained to a plane perpendicular to the z-axis. Options
|
|
<code>distance</code>, <code>angle</code> and <code>torsion</code>, are defined in terms
|
|
of the center of geometry of the specified atom selections.
|
|
Keyword <code>basepair</code> is used to specify a harmonic potential between
|
|
residues <code>isel</code> and <code>jsel</code>. Keywords <code>zaxis</code> and <code>zaxis-cog</code>
|
|
can be used to pull atoms toward the z-axis.
|
|
Option <code>all</code> may be specified to apply an equivalent pmf to each
|
|
of the equivalent solute molecules in the system.
|
|
Option <code>combine</code> may be specified to apply the specified pmf to
|
|
the atoms in all of the equivalent solute molecules.
|
|
Option <code>constraint</code> may be specified to a distance pmf to treat
|
|
the distance as a contraint.
|
|
Option <code>bias</code> may be specified to indicate that this function
|
|
should be treated as a biasing potential. Appropriate corrections
|
|
to free energy results will be evaluated.
|
|
|
|
<P>
|
|
|
|
<H1><A NAME="SECTION003260000000000000000">
|
|
30.6 Generating a restart file</A>
|
|
</H1>
|
|
|
|
<P>
|
|
<PRE>
|
|
new_rst
|
|
</PRE>
|
|
|
|
<P>
|
|
Keyword <code>new_rst</code> will cause an existing restart file to be
|
|
overwritten with a new file.
|
|
|
|
<P>
|
|
The follwing directives control the manipulation of restart
|
|
files, and are executed in the order in which they
|
|
appear in the <B>prepare</B> input deck.
|
|
|
|
<P>
|
|
<PRE>
|
|
solvent name <string*3 slvnam default ``HOH''> \
|
|
model <string slvmdl default ``spce''>
|
|
</PRE>
|
|
|
|
<P>
|
|
The solvent keyword can be used to specify the three letter solvent name
|
|
as expected on the PDB formatted file, and the name of the solvent model
|
|
for which solvent coordinates will be used.
|
|
|
|
<P>
|
|
<PRE>
|
|
solvate [ < real rshell default 1.2 > ] \
|
|
( [ cube [ <real edge> ]] | \
|
|
[ box [ <real xedge> [ <real xedge> [ <real xedge> ]]]] | \
|
|
[ sphere <real radius> ] |
|
|
[ troct <real edge> ])
|
|
</PRE>
|
|
|
|
<P>
|
|
Solvation can be specified to be in a cubic box with specified edge,
|
|
rectangular box with specified edges, or in a sphere with specified
|
|
radius. Solvation in a cube or rectangular box will automatically also
|
|
set periodic boundary conditions. Solvation in a sphere will only allow
|
|
simulations without periodic boundary conditions. The size of the cubic
|
|
and rectangular boxes will be expanded by a length specified by the
|
|
expand variable. If no shape is specified, solvation will be done for
|
|
a cubic box with an edge that leaves rshell nm between any solute atom and
|
|
a periodic image of any solute atom after the solute has been centered.
|
|
An explicit <code>write</code> is not needed to write the restart file.
|
|
The <code>solvate</code> will write out a file <code>sys_calc</code>.rst.
|
|
If not specified, the dimension of the solvation cell will be as large
|
|
as to have at least a distance of <code>rshell</code> nm between any solute atom
|
|
and the edge of the cell. The experimental <code>troct</code> directive generates
|
|
a truncated octrahedral box.
|
|
|
|
<P>
|
|
<PRE>
|
|
touch <real touch default 0.23>
|
|
</PRE>
|
|
|
|
<P>
|
|
The variable <code>touch</code> specifies the minimum distance between a solvent
|
|
and solute atom for which a solvent molecule will be accepted for solvation.
|
|
|
|
<P>
|
|
<PRE>
|
|
envelope <real xpndw default 0.0>
|
|
</PRE>
|
|
sets the expand vealues to be used in <code>solvate</code> operations.
|
|
|
|
<P>
|
|
<PRE>
|
|
expand <real xpndw default 0.1>
|
|
</PRE>
|
|
|
|
<P>
|
|
The variable <code>xpndw</code> specifies the size in nm with which the simulation
|
|
volume will be increased after solvation.
|
|
|
|
<P>
|
|
<PRE>
|
|
read [rst | rst_old | pdb] <string filename>
|
|
write [rst | [solute [<integer nsolvent>]] ( [large] pdb | xyz)] <string filename>
|
|
</PRE>
|
|
|
|
<P>
|
|
These directives read and write the file <code>filename</code> in the specified
|
|
format. The <code>solute</code> option instructs to write out the coordinates
|
|
for solute and all, or if specified the first <code>nsolvent</code>, crystal solvent
|
|
molecules only.
|
|
If no format is specified, it will be derived from the extension of the
|
|
filename. Recognized extensions are rst, rst_old (read only), pdb, xyz
|
|
(write only) and pov (write only).
|
|
Reading and then writing the same restart file will cause the
|
|
sub-block size information to be lost. If this information needs to be
|
|
retained a shell copy command needs to be used.
|
|
The <code>large</code> keyword allows PDB files to be written with more than 9999
|
|
residues. Since the PDB file will not conform to the PDB convention, this
|
|
option should only be used if required. NWChem will be able to read the
|
|
resulting PDB file, but other codes may not.
|
|
|
|
<P>
|
|
<PRE>
|
|
scale <real scale default -1.0>
|
|
</PRE>
|
|
|
|
<P>
|
|
This directive scales the volume and coordinates written to povray files.
|
|
A negative value of scale (default) scales the coordinates to lie
|
|
in [-1:1].
|
|
|
|
<P>
|
|
<PRE>
|
|
cpk [<real cpk default 1.0>]
|
|
</PRE>
|
|
|
|
<P>
|
|
This directive causes povray files to contain cpk model output. The
|
|
optional value is used to scale the atomic radii. A neagtive value
|
|
of cpk resets the rendering to stick.
|
|
|
|
<P>
|
|
<PRE>
|
|
center | centerx | centery | centerz
|
|
</PRE>
|
|
|
|
<P>
|
|
These directives center the solute center of geometry at the origin,
|
|
in the y-z plane, in the x-z plane or in the x-y plane, respectively.
|
|
|
|
<P>
|
|
<PRE>
|
|
orient
|
|
</PRE>
|
|
|
|
<P>
|
|
This directive orients the solute principal axes.
|
|
|
|
<P>
|
|
<PRE>
|
|
translate [atom | segment | molecule] \
|
|
<integer itran> <integer itran> <real xtran(3)>
|
|
</PRE>
|
|
|
|
<P>
|
|
This directive translates solute atoms in the indicated range by xtran,
|
|
without checking for bad contacts in the resulting structure.
|
|
|
|
<P>
|
|
<PRE>
|
|
rotate [atom | segment | molecule] \
|
|
<integer itran> <integer itran> <real angle> <real xrot(3)>
|
|
</PRE>
|
|
|
|
<P>
|
|
This directive rotates solute atoms in the indicated range by angle
|
|
around the vector given by xrot,,
|
|
without checking for bad contacts in the resulting structure.
|
|
|
|
<P>
|
|
<PRE>
|
|
remove solvent [inside | outside] [x <real xmin> <real xmax>] \
|
|
[y <real ymin> <real ymax>] [z <real zmin> <real zmax>]
|
|
</PRE>
|
|
|
|
<P>
|
|
This directive removes solvent molecules inside or outside the
|
|
specified coordinate range.
|
|
|
|
<P>
|
|
<PRE>
|
|
periodic
|
|
</PRE>
|
|
|
|
<P>
|
|
This directive enables periodic boundary conditions.
|
|
|
|
<P>
|
|
<PRE>
|
|
vacuo
|
|
</PRE>
|
|
|
|
<P>
|
|
This directive disables periodic boundary conditions.
|
|
|
|
<P>
|
|
<PRE>
|
|
grid <integer mgrid default 24> <real rgrid default 0.2>
|
|
</PRE>
|
|
|
|
<P>
|
|
This directive specifies the grid size of trial counter-ion positions and
|
|
minimum distance between an atom in the system and a counter-ion.
|
|
|
|
<P>
|
|
<PRE>
|
|
crop
|
|
</PRE>
|
|
prints minimum and maximum solute coordinates.
|
|
|
|
<P>
|
|
<PRE>
|
|
boxsize
|
|
</PRE>
|
|
specifies to redetermine the box size.
|
|
|
|
<P>
|
|
<PRE>
|
|
cube
|
|
</PRE>
|
|
specifies to redetermine the smallest cubic box size.
|
|
|
|
<P>
|
|
<PRE>
|
|
box <real xsize> <real ysize> <real zsize>
|
|
</PRE>
|
|
|
|
<P>
|
|
The <code>box</code> directive resets the box size.
|
|
|
|
<P>
|
|
<PRE>
|
|
align <string atomi> <string atomj> <string atomk>
|
|
</PRE>
|
|
|
|
<P>
|
|
The <code>align</code> directive orients the system such that
|
|
<code>atomi</code> and <code>atomj</code> are on the z-axis, and <code>atomk</code>
|
|
in the x=y plane.
|
|
|
|
<P>
|
|
<PRE>
|
|
repeat [randomx | randomy | randomz] [chains | molecules | fractions ] \
|
|
<integer nx> <integer ny> <integer nz> [<real dist>] [<real zdist>]
|
|
</PRE>
|
|
|
|
<P>
|
|
The <code>repeat</code> directive causes a subsequent <code>write pdb</code>
|
|
directive to write out multiple copies of the system, with <code>nx</code>
|
|
copies in the x, <code>ny</code> copies in the y, and <code>nz</code> copies in
|
|
the z-direction, with a minimum distance of <code>dist</code> between any
|
|
pair of atoms from different copies. If <code>nz</code> is -2, an inverted
|
|
copy is placed in the z direction, with a separation of <code>zdist</code> nm.
|
|
If <code>dist</code> is negative, the box dimensions will be used.
|
|
For systems with solvent, this directive should be used with a negative
|
|
<code>dist</code>.
|
|
Optional keywords <code>chains</code>, <code>molecules</code> and <code>fractions</code>
|
|
specify to write each repeating solute unit as a chain, to repeat
|
|
each solute molecule, or each solute fraction separately. Optional
|
|
keywords <code>randomx</code>, <code>randomy</code>, and <code>randomz</code> can be used
|
|
to apply random rotations for each repeat unit around a vector through
|
|
the center of geometry of the solute in the x, y or z direction.
|
|
|
|
<P>
|
|
<PRE>
|
|
skip <integer ix> <integer iy> <integer iz>
|
|
</PRE>
|
|
|
|
<P>
|
|
The <code>skip</code> directive can be used to skip single repeat unit
|
|
from the <code>repeat</code> directive. Up to 100 <code>skip</code> directives
|
|
may be specified, and will only apply to the previously specified
|
|
<code>repeat</code> directive.
|
|
|
|
<P>
|
|
<PRE>
|
|
(collapsexy | collapsez) [ <integer nmoves>]
|
|
</PRE>
|
|
specifies to move all solute molecules toward the <code>z</code>-axis or
|
|
<code>x=y</code>-plane, respectively, to within a distance of <code>touch</code>
|
|
nm between any pair of atoms from different solute molecules. Parameter
|
|
<code>nmoves</code> specifies the number of collapse moves that will be made.
|
|
Monatomic ions will move with the nearest multi-atom molecule.
|
|
|
|
<P>
|
|
<PRE>
|
|
collapse_group <integer imol> <integer jmol>
|
|
</PRE>
|
|
specifies that molecule jmol will move together with molecule imol in
|
|
collapse operations.
|
|
|
|
<P>
|
|
<PRE>
|
|
merge <real xtran(3)> <string pdbfile>
|
|
</PRE>
|
|
specifies to merge the coordinates found on the specified pdb file
|
|
into the current structure after translation by xtran(3).
|
|
|
|
<P>
|
|
<HR>
|
|
<!--Navigation Panel-->
|
|
<A NAME="tex2html1585"
|
|
HREF="node33.html">
|
|
<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="next.png"></A>
|
|
<A NAME="tex2html1581"
|
|
HREF="user.html">
|
|
<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up.png"></A>
|
|
<A NAME="tex2html1575"
|
|
HREF="node31.html">
|
|
<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="prev.png"></A>
|
|
<A NAME="tex2html1583"
|
|
HREF="node2.html">
|
|
<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="contents.png"></A>
|
|
<BR>
|
|
<B> Next:</B> <A NAME="tex2html1586"
|
|
HREF="node33.html">31. Molecular dynamics</A>
|
|
<B> Up:</B> <A NAME="tex2html1582"
|
|
HREF="user.html">user</A>
|
|
<B> Previous:</B> <A NAME="tex2html1576"
|
|
HREF="node31.html">29. Electrostatic potentials</A>
|
|
  <B> <A NAME="tex2html1584"
|
|
HREF="node2.html">Contents</A></B>
|
|
<!--End of Navigation Panel-->
|
|
<ADDRESS>
|
|
Edoardo Apra
|
|
2004-05-25
|
|
</ADDRESS>
|
|
</BODY>
|
|
</HTML>
|