Analysis Commands
In CHARMM23, new analysis commands are under development, but some
features are currently functional.
* Menu:
* Description:: Description of analysis facility
* Energy:: Energy partitioning
Description of the ANALysis Command
ANALys {ON } Enable analysis and disable FAST routines.
{OFF} Disable analysis and restore FAST option defaults.
The ANALysis command is a new energy and structure table facility that is
being developed to examine both static and dynamic properties. The
current code only allows energy partition analysis and energy contribution
analysis from free energy simulations. It also can produce a detailed
printout of energy term contributions.
Energy option of the ANALysis Command
Syntax:
ANALys { ON }
{ TERM { [ALL] } { NONBond } [UNIT int] atom-selection }
{ { ANY } { [NONOnbond] } }
{ OFF }
The ANALysis ON command enables energy partition analysis and disables the
FAST routines. This will slow the calculation (especially on vector machines),
but allow a detailed, atom by atom, energy analysis. Everytime the energy
routine is invoked, the energy for each atom is stored in the ECONT array.
During PERT dynamics, the EPCONT is filled with the time average energy
difference on a atom by atom basis including every step of dynamics. This
allows the free energy differences to be analyzed based on atom contributions.
The ANALysis TERM command will cause all selected energy terms to be
printed to the specified output unit (default: standard CHARMM output).
The ALL keyword (default) will list elements where all atoms are
selected. The ANY keyword will cause terms including any selected atom
to be listed. The NONOnbond keyword (default) suppresses the listing
of vdw and electrostatic energy terms. The NONBonded keywords also
allows the analysis of vdw and electrostatic interactions.
The ANALys OFF command enables the FAST routines and disables the resetting
of the ECONT array (i.e. the ECONT array will not change, but may still be
accessed. This command also disables the energy term analysis.
The energy partition array can be accessed with the SCALar ECONt
commands. *note Econt:(scalar.doc). The sum of all of the elements
of the ECONT array is usually the total energy, but some energy terms, such
as extended electrostatics, will not be included. The command:
SCALar ECONT STATistics
can be used to check the total energy and the command
SCALar EPCONT ....
can be used to examine atom contributions to energy differences for PERT.
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory