Jones de Andrade wrote:
Hi!
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.
As you discovered below, removing them is not really what you want to do
- you want to calculate the non-bonded interactions for atoms in your
long molecules in two parts. Specifically, they are atom-atom
interactions in the same molecule and atom-atom interaction in other
molecules or solvent. The way to do this is using "energy groups" which
you construct using make_ndx - please try make_ndx and read
documentation for details. Once you've set each molecule up as a
separate group, g_energy will report pairwise total interactions between
all pairs of groups, which you can now add in whatever combination make
sense for what you're trying to do.
Mark
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!
Jones
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