[gmx-users] RE: Doubts over g_lie usage

Tom Dupree t.dupree at unsw.edu.au
Tue Aug 14 07:00:59 CEST 2012

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,

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
-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?


Peterson J

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