<br><font size=2 face="sans-serif">David,</font>
<br>
<br><font size=2 face="sans-serif">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 kJ/mol. </font>
<br>
<br><font size=2 face="sans-serif">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.</font>
<br>
<br><font size=2 face="sans-serif">Ruhong</font>
<br>
<br><font size=2 face="sans-serif">Ruhong Zhou , PhD<br>
Computaional Biology Center <br>
IBM Thomas J. Watson Research Center <br>
Yorktown Heights, NY 10598 <br>
Tel: (914) 945-3591, Fax: (914) 945-4104 <br>
http://www.research.ibm.com/people/r/ruhong <br>
</font>
<br>
<br>
<br>
<table width=100%>
<tr valign=top>
<td>
<td><font size=1 face="sans-serif"><b>David <spoel@xray.bmc.uu.se></b></font>
<br><font size=1 face="sans-serif">Sent by: gmx-users-admin@gromacs.org</font>
<p><font size=1 face="sans-serif">05/18/2003 06:28 PM</font>
<br><font size=1 face="sans-serif">Please respond to gmx-users</font>
<td><font size=1 face="Arial"> </font>
<br><font size=1 face="sans-serif"> To:
gmx-users@gromacs.org</font>
<br><font size=1 face="sans-serif"> cc:
</font>
<br><font size=1 face="sans-serif"> Subject:
Re: [gmx-users] How to print out vdw-14
energy terms for each pair in minimization?</font></table>
<br>
<br>
<br><font size=2><tt>On Sun, 2003-05-18 at 22:13, Ruhong Zhou wrote:<br>
> Hi,<br>
> <br>
> How to print out the vdw-14 energy terms for each pair in the first<br>
> step of minimization? I found that the total vdw-14 interaction energy<br>
> for a ligand (bound to Ribonuclease A) in GROMACS using OPLSAA force<br>
> field is different from that of IMPACT, while the other energy terms<br>
> are all the same, including the elec-14 energy. The topology file
was<br>
> converted from the OPLSAA atomtyping code I wrote a while ago, and
it<br>
> seems working fine for another ligand DHAP bounding to enzymeTIM (all<br>
> energy terms are the same for the ligand). So I am confused what else<br>
> could be wrong. I quickly checked some key LJ parameters, and
they<br>
> are the same in GROMACS database files and the "official"
OPLSAA2000<br>
> in IMPACT. Thus, I would like to print out each pair's energy term
to<br>
> see where the problem could be.<br>
There is no direct method to do it. Have you verified that the recently<br>
discussed error in ffoplsaa.itp (combinationrule should be three rather<br>
than two) is fixed?<br>
<br>
You should maybe check the pair (vdw1-4) parameters in the tpr file,<br>
using gmxdump -s topol.tpr | more <br>
search for idef<br>
<br>
<br>
-- <br>
Groeten, David.<br>
________________________________________________________________________<br>
Dr. David van der Spoel,
Dept. of Cell and Molecular Biology<br>
Husargatan 3, Box 596,
75124 Uppsala, Sweden<br>
phone:
46 18 471 4205
fax: 46 18 511 755<br>
spoel@xray.bmc.uu.se
spoel@gromacs.org http://xray.bmc.uu.se/~spoel<br>
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