|
enseval.pl
Usage
usage: enseval.pl [options] tag options: [-par CHARMMparams] [-set proptag=value,...] [-overwrite] [-run [from:]to] [-dir workdir] [-update frq] [PARALLELoptions] [-log file] [-custom file] [-charmmexec charmmexec]
Description
This script is used to evaluate all-atom energies with CHARMM for ensemble
structures. The options -par, -run, -dir, -log
and the options for parallel execution function the same way as in ensmin.pl but only a single tag is needed here because new structures are not generated.
For each structure in the ensemble an energy evaluation is carried out according
to the CHARMM parameters
given with -par. According to the assignment list given with -set
the total energy or components of it are then stored as ensemble data. The comma-separated
list consists of pairs of property tags and energy component names as in
enerCHARMM.pl.
By default, a property value that has been set previously is not overwritten but th
option -overwrite is available if values that may be present already should be
replaced with new values.
The option -update can be used to set the frequency with which the ensemble
data file is updated. By default this number is set to 10. If quick energy evaluations
are run in parallel on many nodes this may cause an I/O bottle neck on the server
and it is advisable to use larger update frequencies between 50 and 1000 under
these circumstances.
This command does not carry out any minimization or other refinement and only
evaluates single-point energies like <docmark>enerCHARMM.pl</docmark>. An ensemble
of structures can be minimized with <docmark>ensmin.pl</docmark> if necessary.
Options
- -help
- usage information
Examples
enseval.pl -dir data -run 5 -set erdie=total -par param=19,dielec=rdie,epsilon=4.0 vacmin
evaluates CHARMM energies for the 5 ensemble structures under the
tag vacmin in the data directory.
Energies are calculated with distance dependent dielectric and an
epsilon value of 4.0. The total energy is then stored under the
property tag erdie.