[gmx-users] Values for pairs, when attached to the topology...?
mgoette at mpi-bpc.mpg.de
Fri May 13 14:49:01 CEST 2005
I have a problem with parameters, manually included to the pairs
section. For FEP purposes, I have(?) to include the pair parameters for
the perturbed atoms ((A and B value) into the topology file (OPLSAA FF).
I took the values eps and sig for the two atoms i and j from the
nonbonded topology, calculated the ij value via the formulas in the
manual and inserted these values for eps and sig in the topology file.
mdrun claims, that the parameters are wrong:
Fatal error: Force field inconsistency: 1-4 interaction parameters for
atoms 1615-1621 not the same as for other atoms with the same atom type
Obviously, the parameters, I calculated are wrong. Do I have to include
fudge-factors in my calculations ?
I am also not sure, if there have to be c6 and c12 in the topology file,
or if eps and sig are ok.
Please give me some information, how the parameters out of the
forcefield have to be calculated correctly and which ones I have to use
in my topology file
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
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