[gmx-users] How to print out vdw-14 energy terms for each pair in minimization?

Ruhong Zhou ruhongz at us.ibm.com
Sun May 18 22:10:01 CEST 2003


How to print out the vdw-14 energy terms for each pair in the first step 
of minimization? I found that the total vdw-14 interaction energy for a 
ligand (bound to Ribonuclease A) in GROMACS using OPLSAA force field is 
different from that of IMPACT, while the other energy terms are all the 
same, including the elec-14 energy. The topology file was converted from 
the OPLSAA atomtyping code I wrote a while ago, and it seems working fine 
for another ligand DHAP bounding to enzymeTIM (all energy terms are the 
same for the ligand). So I am confused what else could be wrong.  I 
quickly checked some key LJ parameters, and they are the same in GROMACS 
database files and the "official" OPLSAA2000 in IMPACT. Thus, I would like 
to print out each pair's energy term to see where the problem could be.



Ruhong Zhou , PhD
Computaional Biology Center 
IBM Thomas J. Watson Research Center 
Yorktown Heights,  NY 10598 
Tel: (914) 945-3591, Fax: (914) 945-4104 
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