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

[Mark Abraham]

Hi,

I think that is the behaviour, though the wording of manual 5.7.1 leaves a
lot to be desired... I'd fix it, but I've never played with the feature,
nor looked at that code!

Mark

On Sat, May 23, 2015 at 7:34 PM Lee-Ping Wang <leeping at stanford.edu> wrote:

> Hi Mark,
>
> 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
> behavior?
>
> Thanks,
>
> - Lee-Ping
>
> -----Original Message-----
> 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
> Abraham
> 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
>
> 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
> >
> >
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a
> mail to gmx-users-request at gromacs.org.
>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>