[gmx-users] Doubts over g_lie usage

[J Peterson]

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




--
View this message in context: http://gromacs.5086.n6.nabble.com/Doubts-over-g-lie-usage-tp5000130.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.