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g_ffscan_d

NAME

g_ffscan - scan and modify force field data for a single point energy calculation

SYNOPSIS

g_ffscan -s topol.tpr -g md.log -table table.xvg -parm params.dat -ga genalg.dat -c junk.gro -e junk.edr -o junk.trr -[no]h -nice int -[no]xvgr -tol real -fmax real -[no]comb -npow real -[no]logeps -[no]v -epot real -fepot real -pres real -fpres real -fmsf real -molsize int -nmol int

DESCRIPTION

The g_ffscan program performs a single point energy and force calculation in which the force field is modified. This way a range of parameters can be changed and tested for reproduction of e.g. quantum chemical or experimental data. A grid scan over the parameters is done as specified using command line arguments. All parameters that reproduce the energy within a given absolute tolerance are printed to a log file.

Obviously polarizable models can be used, and shell optimisation is performed if necessary. Also, like in mdrun table functions can be used for user defined potential functions.

If the option -ga with appropriate file is passed, a genetic algorithm will be used rather than a grid scan.

FILES

-s topol.tpr Input
 Generic run input: tpr tpb tpa xml 

-g md.log Output
 Log file 

-table table.xvg Input, Opt.
 xvgr/xmgr file 

-parm params.dat Input
 Generic data file 

-ga genalg.dat Input, Opt.
 Generic data file 

-c junk.gro Output
 Coordinate file in Gromos-87 format 

-e junk.edr Output
 Generic energy: edr ene 

-o junk.trr Output
 Full precision trajectory: trr trj 

OTHER OPTIONS

-[no]h no
 Print help info and quit

-nice int 19
 Set the nicelevel

-[no]xvgr yes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-tol real 0.1
 Energy tolerance (kJ/mol) (zero means everything is printed)

-fmax real 100
 Force tolerance (zero means everything is printed)

-[no]comb yes
 Use combination rules

-npow real 12
 Power for LJ in case of table use

-[no]logeps no
 Use a logarithmic scale for epsilon

-[no]v no
 Be loud and noisy

-epot real 0
 Target energy (kJ/mol)

-fepot real 1
 Factor for scaling energy violations (0 turns energy contribution off)

-pres real 1
 Value for reference pressure

-fpres real 0.1
 Factor for scaling pressure violations (0 turns pressure contribution off)

-fmsf real 0.1
 Factor for scaling mean square force violations (0 turns MSF contribution off)

-molsize int 1
 Number of atoms per molecule

-nmol int 1
 Number of molecules (Epot is divided by this value!)

SEE ALSO

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.