[gmx-users] non-bonded interactions in GROMACS

[T. Zaraiskaya]

hello all,
I wonder if you can help me to understand nonbonded interactions
in GROMACS?

1.Are coulomb interactions excluded from 1-2, 1-3 and 1-4 interactions?
 L-J are excluded from interactions between first and second bonded neighbours
and scaled for 1-4 pairs, what about Coulomb, there is
nothing in manual about it.

2. I am doing energy minimization, steep algorithm, lipid FF is taken
from ffG43a2x, generate pairs = no.
When some pairs ( e.g. H - CH1, both atoms with positive charges) are included
in [pairs] section of the topology with c6 and c12 =0, i am getting a
positive  pot.energy; when these
pairs (with c6,c12=0) are not listed in [pairs] the pot. energy has a negative
value, the term which is changing is Coulomb1-4. This is confusing
because if Coulomb1-4 interactions were excluded or scaled
by default i would expect to see smaller Coulomb1-4 term when these pairs are included.

  How to include nonbond.1-4 interactions correctly? Include pairs
with c6,c12=0 in [pairs]? Place them into [exclusions]?
something else...?

What exactly happens when I use option  -check14 of grompp?
Are Coulomb interactions in 1-4 pairs removed as well,
I guess this question recurse to previous.

thanks in advance,


=============
Tanya Zaraiskaya
Department of Physics
University of Guelph
Guelph  ON  N1G 2W1
CANADA
email: tz at physics.uoguelph.ca
phone: (519)824-4120 x8346.