[gmx-users] Intra x inter coulombic and van-der-waals terms

Jones de Andrade johannesrs at gmail.com
Thu May 4 21:46:15 CEST 2006


Well, I was trying to calculate the intermolecular total energy of
some long systems here, when I got locked in a problem.

g_energy allows me to isolate Coulomb-(SR), Coulomb-14 and
Coul.-recip. for the coulombic terms, for example. The seems to be
that, in long chain molecules (by long, I mean more than 1-4 maximum
distance), the program outputs the 1-n (n>4) intramolecular terms of
the interactions together with most of the other intermolecular
coulombic terms in Coulomb-(SR) (exception for the molecules so far
that are in the Coul.-recip. part, but my molecules are some times
smaller than any cutoff radius used).

I would like to know if there is any work-around for this, in order to
remove the 1-n (n>4) intramolecular terms from the other
intermolecular total energies I get.

Just in time: I tried to increase, in the topology file, the nrexcl
(to 9, the largest number of bonds between two atoms in the molecules
simulated) parameter. It helped a lot, and started to yeld really
better values. But, on the other hand, it also yelded very different
trajectories, probably due to changes in conformation as a consequence
of the lack of forces derived from those intramolecular interactions
it excluded.  :(

Does anybody have any idea of how to deviate from this problem?

Thanks a lot in advance!


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