You need to assign your own experimentally determined values to -Elj and -Eqq.
These are determined by simulating your ligand in a solvent box.
g_lie uses some common values found in the literature for -Clj and -Cqq again
you need to decide if they are appropriate in your case. Try reading papers by
Aquvist et al to help with this.
Individual average values can be calculated using the LJ and Coul
energies/forces from your energy file and following the LIE equation.
Beware of using g_lie if you have used PME for your electrostatics.
Have fun,
Tom
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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