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Difference between revisions of "enseval.pl"
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This script is used to evaluate all-atom energies with CHARMM for ensemble | This script is used to evaluate all-atom energies with CHARMM for ensemble | ||
structures. The options <B>-par</B>, <B>-run</B>, <B>-dir</B>, <B>-log</B> | structures. The options <B>-par</B>, <B>-run</B>, <B>-dir</B>, <B>-log</B> | ||
− | and the options for | + | and the options for [http://feig.bch.msu.edu/mmtsb/PARALLELoptions parallel execution] function the same way as in [[ensmin.pl]] but only a single tag is needed here because new structures are not generated.<BR><BR> |
− | |||
− | function the same way as in | ||
− | tag is needed here because new structures are not generated.<BR><BR> | ||
For each structure in the ensemble an energy evaluation is carried out according | For each structure in the ensemble an energy evaluation is carried out according | ||
− | to the | + | to the [http://feig.bch.msu.edu/mmtsb/CHARMM_Parameters CHARMM parameters] |
given with <B>-par</B>. According to the assignment list given with <B>-set</B> | given with <B>-par</B>. According to the assignment list given with <B>-set</B> | ||
− | the total energy or components of it are then stored as ensemble data. The comma-separated | + | 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]]. |
− | list consists of pairs of property tags and energy component names as in | + | |
− | + | By default, a property value that has been set previously is not overwritten but the option <B>-overwrite</B> is available if values that may be present already should be replaced with new values.<BR><BR> | |
− | By default, a property value that has been set previously is not overwritten but | + | The option <B>-update</B> 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.<BR><BR> |
− | option <B>-overwrite</B> is available if values that may be present already should be | ||
− | replaced with new values.<BR><BR> | ||
− | The option <B>-update</B> 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.<BR><BR> | ||
This command does not carry out any minimization or other refinement and only | This command does not carry out any minimization or other refinement and only | ||
− | evaluates single-point energies like | + | evaluates single-point energies like [[enerCHARMM.pl]]. An ensemble |
− | of structures can be minimized with | + | of structures can be minimized with [[ensmin.pl]] if necessary. |
== Options == | == Options == | ||
; -help : usage information | ; -help : usage information | ||
− | + | ; -par key=value[,...] : CHARMM parameters | |
+ | ; -set name=value[,...] : assign properties based on CHARMM energy values | ||
+ | ; -run [from:]to : minimize only subset of structures | ||
+ | ; -natpdb pdbFile : provide reference structure for automatic RMSD calculation | ||
+ | ; -dir directory : data directory | ||
+ | ; -[no]compress : (do not) compress minimized structures | ||
+ | ; -update frq : update frequency for property file in parallel calculations | ||
+ | ; -log file : output log file | ||
== Examples == | == Examples == | ||
<mmtsbToolExample cmd="enseval.pl" set="/apps/mmtsb/bench/enseval.pl-test/test1"></mmtsbToolExample> | <mmtsbToolExample cmd="enseval.pl" set="/apps/mmtsb/bench/enseval.pl-test/test1"></mmtsbToolExample> |
Latest revision as of 12:43, 30 July 2009
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 the 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 enerCHARMM.pl. An ensemble
of structures can be minimized with ensmin.pl if necessary.
Options
- -help
- usage information
- -par key=value[,...]
- CHARMM parameters
- -set name=value[,...]
- assign properties based on CHARMM energy values
- -run [from:]to
- minimize only subset of structures
- -natpdb pdbFile
- provide reference structure for automatic RMSD calculation
- -dir directory
- data directory
- -[no]compress
- (do not) compress minimized structures
- -update frq
- update frequency for property file in parallel calculations
- -log file
- output log file
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.