Difference between revisions of "equiCHARMM.pl"

Latest revision as of 01:00, 1 August 2009

Usage

usage:    equiCHARMM.pl [options] PDBfile
options:  [-prefix filename] [-logs] [-trajs] [-cmds]
          [-par CHARMMparams]
          [-cons [ca|cb|cab|heavy] refpdb|self min:max[_force][=...]]
          [-fixsolute] [-densitysteps value]
          [-equi temp:steps[=temp:steps]]
          [-cubicbox] [-octabox] [-cutoff value]
          [-neutralize] [-addions concentration]
          [-[no]center]
          [-custom file]
          [-verbose]

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Description

This script will automatically setup, heatup, and equilibrate a given solute in explicit solvent. The final structure is meant to serve as a starting structure for production moelcular dynamics runs.

Options

-help: usage information
-prefix name: prefix for output files
-logs: generate CHARMM log files at each stage
-trajs: generate trajectory files at each stage
-cmds: generate CHARMM input files at each stage
-par key=value[,...]: CHARMM parameters
-l [ca|cb|cab|heavy] force refpdb|self min:max[=...]: apply restraints to atoms outside specified residue range
-cons [ca|cb|cab|heavy] refpdb|self min:max[_force][=...]: apply restraints to specified residue range
-fixsolute: fix solute atoms
-densitysteps value: number of time steps during simulation for estimating solent density
-equi temp:steps[=temp:steps ...]: heating protocol
-cubicbox: solvate in cubic box
-octabox: solvate in ocatahedron
-cutoff value: minimum distance from solute to edge of solvation box
-neutralize: add counterions to neutralize system
-addions concentraion: add NaCl ion pairs to reach given concentration
-custom file: provide custom CHARMM input file
-verbose: provide extensive information about progress of equilibration

@@ Line 6: / Line 6: @@
 == Description ==
+This script will automatically setup, heatup, and equilibrate a given solute in explicit solvent. The final structure is meant to serve as a starting structure for production moelcular dynamics runs.
 == Options ==
 ; -help : usage information
+; -prefix name : prefix for output files
+; -logs : generate CHARMM log files at each stage
+; -trajs : generate trajectory files at each stage
+; -cmds : generate CHARMM input files at each stage
+; -par key=value[,...] : CHARMM parameters
+; -l [ca|cb|cab|heavy] force refpdb|self min&#58;max[=...] : apply restraints to atoms outside specified residue range
+; -cons [ca|cb|cab|heavy] refpdb|self min&#58;max[_force][=...] : apply restraints to specified residue range
+; -fixsolute : fix solute atoms
+; -densitysteps value : number of time steps during simulation for estimating solent density
+; -equi temp&#58;steps[=temp&#58;steps ...] : heating protocol
+; -cubicbox : solvate in cubic box
+; -octabox : solvate in ocatahedron
+; -cutoff value : minimum distance from solute to edge of solvation box
+; -neutralize : add counterions to neutralize system
+; -addions concentraion : add NaCl ion pairs to reach given concentration
+; -custom file : provide custom CHARMM input file
+; -verbose : provide extensive information about progress of equilibration
 == Examples ==