g_lie(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_lie(1)NAME
g_lie - free energy estimate from linear combinations
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_lie -f ener.edr -o lie.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -Elj real -Eqq real -Clj real -Cqq
real -ligand string
DESCRIPTION
g_lie computes a free energy estimate based on an energy analysis from. One needs an energy file with the following components: Coul (A-B)
LJ-SR (A-B) etc.
FILES -f ener.edr Input
Energy file
-o lie.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 19
Set the nicelevel
-b time 0
First frame (ps) to read from trajectory
-e time 0
Last frame (ps) to read from trajectory
-dt time 0
Only use frame when t MOD dt = first time (ps)
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-Elj real 0
Lennard-Jones interaction between ligand and solvent
-Eqq real 0
Coulomb interaction between ligand and solvent
-Clj real 0.181
Factor in the LIE equation for Lennard-Jones component of energy
-Cqq real 0.5
Factor in the LIE equation for Coulomb component of energy
-ligand string none
Name of the ligand in the energy file
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_lie(1)
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g_enemat(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_enemat(1)NAME
g_enemat - extracts an energy matrix from an energy file
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_enemat -f ener.edr -groups groups.dat -eref eref.dat -emat emat.xpm -etot energy.xvg -[no]h -[no]version -nice int -b time -e time -dt
time -[no]w -xvg enum -[no]sum -skip int -[no]mean -nlevels int -max real -min real -[no]coul -[no]coulr -[no]coul14 -[no]lj -[no]lj
-[no]lj14 -[no]bhamsr -[no]bhamlr -[no]free -temp real
DESCRIPTION
g_enemat extracts an energy matrix from the energy file ( -f). With -groups a file must be supplied with on each line a group of atoms
to be used. For these groups matrix of interaction energies will be extracted from the energy file by looking for energy groups with names
corresponding to pairs of groups of atoms, e.g. if your -groups file contains:
2
Protein
SOL
then energy groups with names like 'Coul-SR:Protein-SOL' and 'LJ:Protein-SOL' are expected in the energy file (although g_enemat is most
useful if many groups are analyzed simultaneously). Matrices for different energy types are written out separately, as controlled by the
-[no]coul, -[no]coulr, -[no]coul14, -[no]lj, -[no]lj14, -[no]bham and -[no]free options. Finally, the total interaction energy
energy per group can be calculated ( -etot).
An approximation of the free energy can be calculated using: E(free) = E0 + kT log( exp((E-E0)/kT) ), where '' stands for time-average. A
file with reference free energies can be supplied to calculate the free energy difference with some reference state. Group names (e.g.
residue names) in the reference file should correspond to the group names as used in the -groups file, but a appended number (e.g. residue
number) in the -groups will be ignored in the comparison.
FILES -f ener.edr Input, Opt.
Energy file
-groups groups.dat Input
Generic data file
-eref eref.dat Input, Opt.
Generic data file
-emat emat.xpm Output
X PixMap compatible matrix file
-etot energy.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 19
Set the nicelevel
-b time 0
First frame (ps) to read from trajectory
-e time 0
Last frame (ps) to read from trajectory
-dt time 0
Only use frame when t MOD dt = first time (ps)
-[no]wno
View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-[no]sumno
Sum the energy terms selected rather than display them all
-skip int 0
Skip number of frames between data points
-[no]meanyes
with -groups extracts matrix of mean energies instead of matrix for each timestep
-nlevels int 20
number of levels for matrix colors
-max real 1e+20
max value for energies
-min real -1e+20
min value for energies
-[no]coulyes
extract Coulomb SR energies
-[no]coulrno
extract Coulomb LR energies
-[no]coul14no
extract Coulomb 1-4 energies
-[no]ljyes
extract Lennard-Jones SR energies
-[no]ljno
extract Lennard-Jones LR energies
-[no]lj14no
extract Lennard-Jones 1-4 energies
-[no]bhamsrno
extract Buckingham SR energies
-[no]bhamlrno
extract Buckingham LR energies
-[no]freeyes
calculate free energy
-temp real 300
reference temperature for free energy calculation
SEE ALSO gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_enemat(1)