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

Jones de Andrade johannesrs at gmail.com
Fri May 5 04:54:54 CEST 2006


Sorry if this message reaches the list twice, but Gmail doesn't let me know
if the list received it... seems that it stores somehow in the same message
if it comes back, so I just know when there are answers. :(

Anyway, thanks a lot in advance for any help in this subject!





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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