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

[David]

On Sun, 2003-05-18 at 22:13, Ruhong Zhou wrote:
> Hi,
> 
> 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.
There is no direct method to do it. Have you verified that the recently
discussed error in ffoplsaa.itp (combinationrule should be three rather
than two) is fixed?

You should maybe check the pair (vdw1-4) parameters in the tpr file,
using gmxdump -s topol.tpr | more 
search for idef


-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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