CHARMM Element doc/analys.doc 1.1#File: analys, Node: Top, Up: (chmdoc/commands.doc), Next: Description Analysis Commands The ANALysis command is an energy and structure analysisfacility that has been developed to examine both static and dynamicproperties. The current code allows energy partition analysis andenergy contribution analysis from free energy simulations. It alsocan produce a detailed printout of structural and energy termcontributions for selected atoms* Menu:* Description:: Description of analysis facility* Energy:: Energy partitioning#File: analys, Node: Description, Up: Top, Previous: Top, Next: Energy Description of the ANALysis CommandSyntax:ANALys { ON } { TERM { [ALL] } { NONBond } [UNIT int] atom-selection } { { ANY } { [NONOnbond] } } { OFF }ON Enable energy partition analysis and disable FAST routines.OFF Disable analysis and restore FAST option defaults.TERM Setup energy term print data and disable FAST routines.ALL (default) Print energy terms involving only selected atomsANY Print energy terms when any of the atoms is selectedNONBond In addition to internal terms, also print nonbond termsNONOnbond (default) Do not print electrostatic and vdw energy dataUNIT integer Write the energy term printout data to a formatted file Otherwise, write data to the output file.#File: analys, Node: Energy, Up: Top, Previous: Description, Next: Top Energy term option of the ANALysis CommandThe ANALysis ON command enables energy partition analysis and disables theFAST routines. This will slow the calculation (especially on vector machines),but allows a detailed, atom by atom, energy analysis. Everytime the energyroutine is invoked, the energy for each atom is stored in the ECONT array.During PERT dynamics, the EPCONT is filled with the time average energydifference on a atom by atom basis including every step of dynamics. Thisallows the free energy differences to be analyzed based on atom contributions. The energy partition array can be accessed with the SCALar ECONtcommands. *note Econt:(chmdoc/scalar.doc). The sum of all of the elementsof the ECONT array is usually the total energy, but some energy terms, suchas extended electrostatics, will not be included. The command: SCALar ECONT STATisticscan be used to check the total energy and the command SCALar EPCONT ....can be used to examine atom contributions to energy differences for PERT.The ANALysis TERM command will cause all selected energy terms to beprinted to the specified output unit (default: standard CHARMM output).The ALL keyword (default) will list elements where all atoms areselected. The ANY keyword will cause terms including any selected atomto be listed. The NONOnbond keyword (default) suppresses the listingof vdw and electrostatic energy terms. The NONBonded keywords alsoallows the analysis of vdw and electrostatic interactions.The ANALys OFF command enables the FAST routines and disables the resettingof the ECONT array (i.e. the ECONT array will not change, but may still beaccessed. This command also disables the energy term
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