[gmx-users] How to print out vdw-14 energy terms for each pair in minimization?
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 20 13:24:00 CEST 2003
On Mon, 2003-05-19 at 17:47, Anton Feenstra wrote:
> Ruhong Zhou wrote:
> > David,
> > 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.
> > 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.
> While we're at this subject, in general terms it would be good to have
> a tool that parses the topology and parameters, and prints out the energy
> values for each of the interactions defined. That would be wonderful for
> all sorts of topology and/or forcefield debugging. If I run into something
> like this soon, I might write it myself, otherwise I challenge anybody to
> beat me to it! :-)
That would be excellent for debugging rotten starting structures too.
Call it g_strain
Dr. David van der Spoel, Dept. of Cell & Mol. 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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