[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 23:09:00 CEST 2003


Thanks for the quick reply. The LJ combining rule has been fixed a while 
ago, also this is not due to the Kcal/mol -> KJ/mol conversion factor 
(4.1868 vs. 4.184 I found a while ago).  In fact, the energy difference 
for LJ14 is quite large for this ligand. The Gromacs's LJ14 energy is 
1403.2 KJ/mol, while the IMPACT value is only 48.13 Kcal/mol =  201.37 

Is there a way that I can easily modify the source and print out each 
energy term? If yes, which files should I moidfy? Thanks. I also checked 
tpr file using gmxdump, but no obvious problems found.


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

David <spoel at xray.bmc.uu.se>
Sent by: gmx-users-admin at gromacs.org
05/18/2003 06:28 PM
Please respond to gmx-users
        To:     gmx-users at gromacs.org
        Subject:        Re: [gmx-users] How to print out vdw-14 energy 
terms for each pair     in minimization?

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 
Husargatan 3, Box 596,                   75124 Uppsala, Sweden
phone:           46 18 471 4205                          fax: 46 18 511 
spoel at xray.bmc.uu.se             spoel at gromacs.org   
gmx-users mailing list
gmx-users at gromacs.org
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20030518/899c5b38/attachment.html>

More information about the gromacs.org_gmx-users mailing list