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This commit is contained in:
Tjerk Straatsma 2001-11-06 16:43:21 +00:00
parent a5ee75d686
commit 4e1b1d246f
3 changed files with 48 additions and 19 deletions
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6
doc/user/analysis.tex
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@ -148,14 +148,16 @@ Analyses can be applied to a selection of solute atoms and solvent molecules.
The selection is determined by
\begin{verbatim}
select ( [ <integer isgm> [ <integer jsgm> ]] [ { <string atom> } ] |
select ( [ super ] [ <integer isgm> [ <integer jsgm> ]] [ { <string atom> } ] |
solvent <real range> | save <string filename> | read <string filename> )
\end{verbatim}
where {\rm isgm} is the first segment number, {\rm jsgm} is the last
segment number in the selection, and {\rm \{atom\}} is the set of atom
names selected from the specified residues. By default all solute
atoms are selected.
atoms are selected. When keyword \verb+super+ is specified the selecion
applies to the superimposition option.
\par
For example, all protein backbone atoms are selected by

6
doc/user/nwmd.tex
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@ -605,13 +605,15 @@ will change from \verb+tmpext+ to \verb+tempext2+ between simulation time
\item
\begin{verbatim}
isobar [<real prsext>] [trelax <real prsrlx> ] \
[compres <real compr>] [anisotropic] [noz]
[compres <real compr>] [anisotropic] [xy] [z]
\end{verbatim}
specifies a constant pressure ensemble using Berendsen's piston,
where \verb+<prsext>+ is the external pressure with a default of 1.025~10$^5$ Pa,
\verb+<prsrlx>+ is the pressure relaxation time in ps with a default of 0.5, and
\verb+<compr>+ is the system compressibility in m$^2$N$^{-1}$ with a
default of 4.53E-10.
default of 4.53E-10. Optional keywords \verb+xy+ and \verb+z+ may be used to
specify that pressure scaling is to be applied in the x and y or z dimension
only, respectively.
\end{description}
\section{Velocity reassignments}

55
doc/user/prepare.tex
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@ -93,22 +93,40 @@ 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).
\item[{\bf *}]
{\bf contributed}\\
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).
\item[{\bf *}]
{\bf user preferences}\\
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.
These directories may contain fragment files (with extension frg),
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).
\item[{\bf *}]
{\bf temporary files}\\
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 be such a directory for each supported
force field. These directories may contain fragment files (with extension frg),
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). If not specified, temporary
of the force field and with extension par).
\item[{\bf *}]
{\bf current files}\\
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.
\end{itemize}
@ -117,7 +135,10 @@ 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.
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.
\par
The most common problems with the \prepare\ module are
\begin{itemize}
@ -153,14 +174,15 @@ This entry specifies the default force field. Database files supplied with
to AMBER95, and {\bf charmm}, referring to the academic CHARMM22 force field.
\begin{verbatim}
<string ffname>_(s | x | u | t) <string ffdir>
<string ffname>_(s | x | q | u | t | c) <string ffdir>[<string parfile>]
\end{verbatim}
Entries of this type specify the directory \verb+ffdir+ in which force field
database files can be found.
database files can be found. Optionally the parameterfile in this directory
may be specified as \verb+parfile+.
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 temporary files is specified.
will be used if no directory with current files is specified.
\begin{verbatim}
<string solvnam> <string solvfil>
@ -173,9 +195,9 @@ An example file \$HOME/.nwchemrc is:
\begin{verbatim}
ffield amber
amber_s /msrc/proj/nwchem/share/amber/amber_s/
amber_s /msrc/proj/nwchem/share/amber/amber_s/amber99.par
amber_x /msrc/proj/nwchem/share/amber/amber_x/
amber_u /usr/people/d3j191/data/amber/amber_u/
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/
@ -345,15 +367,18 @@ Currently \amber\ and \charmm\ are the supported force fields.
A default force field may be specified in the file \$HOME/.nwchemrc.
\begin{verbatim}
standard <string dir_s>
extensions <string dir_x>
user <string dir_u>
temporary <string dir_t>
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>]
\end{verbatim}
The user can explicitly specify the directories where force field
specific databases can be found. These include force field standards,
extensions, user preferences and temporary database files.\\
extensions, quality assurance tests, user preferences, temporary , and
current database files.\\
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 \prepare\ module are