[gmx-users] 1-4 interactions in a small molecule are missing

[Mark Abraham]

Hi,

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.

Mark

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.
> When
> I run gmxdump on my .tpr file, it does not output any LJ14 interactions.
> It
> 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:
> https://dl.dropboxusercontent.com/u/5381783/zerotor_excl3.tar.gz
>
>
>
> 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.
>
>
>
> Thanks,
>
>
>
> -          Lee-Ping Wang
>
>
>
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