Hello everyone,
I have a doubt about LIE calculation using g_lie in gromacs. This doubt is
about the values automatically assigned for -Clj and -Cqq flags when I ran
the following command:
$ g_lie -f J32_md10ns.edr -o LIE_1A1_J32.xvg -b 7001 -e 10000 -ligand J32
The following text contains my options and the values automatically assigned
for -Clj and -Cqq
:-) g_lie (-:
Option Filename Type Description
------------------------------------------------------------
-f J32_md10ns.edr Input Energy file
-o LIE_1A1_J32.xvg Output xvgr/xmgr file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-b time 7001 First frame (ps) to read from trajectory
-e time 10000 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w bool no 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 J32 Name of the ligand in the energy file
Opened J32_md10ns.edr as single precision energy file
Using the following energy terms:
LJ: LJ-SR:J32-SOL LJ-LR:J32-SOL LJ-14:J32-SOL
Coul: Coul-SR:J32-SOL Coul-14:J32-SOL
Back Off! I just backed up LIE_1A1_J32.xvg to ./#LIE_1A1_J32.xvg.3#
Last energy frame read 10000 time 10000.000
DGbind = -49.210 (5.282)
More questions are 1. Is the DGbind value here is the overall average of LJ
and Coul ?
2. If that is the case how can I calculate
individual average values for LJ and Coul?
3. How are the 0.181 and 0.5 values for -Clj and
-Cqq assigned?
Thanks,
Peterson J
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