[gmx-users] 1-4 interactions in a small molecule are missing
leeping at stanford.edu
Sat May 23 19:33:59 CEST 2015
Thanks for the explanation, and I tried your suggestion. The energy with
setting "nrexcl = 2" is different from "nrexcl = 3", but changing fudgeLJ
and fudgeQQ does not affect the energy in either case. There are still no
Coulomb-14 and LJ-14 energy terms from g_energy.
I think what's happening is that when I set "nrexcl = 2", Gromacs calculates
the full nonbonded interaction between pairs of atoms separated by 3 bonds,
rather than a "1-4 interaction" which is counted as a different energy term
and is scaled by fudgeLJ and fudgeQQ.
This leads me to conclude that there are no 1-4 pairs created when
gen_pairs=yes in grompp. gen_pairs=yes only generates the pair _parameters_
from the atom types, but not the pairs themselves. There are only 1-4 pairs
when there's a "[ pairs ]" section explicitly defined in the topology file,
which pdb2gmx auto-generates for proteins for example. Is this the expected
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark
Sent: Saturday, May 23, 2015 9:58 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] 1-4 interactions in a small molecule are missing
nrexcl = 3 means to exclude non-bonded interactions up to 3 bonds away, so
you're getting the "no 1-4 interactions" behaviour for which you
inadvertently asked. So set it to 2 and see how you go.
On Sat, May 23, 2015 at 6:44 PM Lee-Ping Wang <leeping at stanford.edu> wrote:
> Hi everyone,
> I've been trying to understand an issue I've had with a simple
> molecule in Gromacs (just 20 atoms) where gen_pairs=yes, nrexcl=3 and
> all of the atoms carry some charge. The system is non-periodic with
> no cutoff. This is a minimal test case derived from a more complex
> system (a lipid bilayer) where I first saw this issue.
> My issue is that there is no "Coulomb-14" or "LJ-14" energy term, and
> the potential energy does not depend on my setting of fudgeLJ and fudgeQQ.
> I run gmxdump on my .tpr file, it does not output any LJ14 interactions.
> does print out the value of fudgeQQ but this value doesn't have an
> effect on the potential energy.
> I thought that this molecule should have some 1-4 interactions because
> there are several pairs of atoms that are separated by three bonds,
> and both atoms have nonzero charge and LJ parameters. I also wrote a
> Python script to calculate the Coulomb and LJ energy just for this
> system, and I confirmed that Gromacs was behaving as if fudgeLJ and
> fudgeQQ were both set to zero.
> My example calculations are archived and documented here:
> If someone more experienced with Gromacs could look at my files and
> explain how I'm misunderstanding the generation and treatment of 1-4
> pairs in Gromacs, I would highly appreciate it.
> - Lee-Ping Wang
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