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

[Lee-Ping Wang]

Hi Mark,

Ah, thanks for the explanation.  Everything makes sense now.  

I think that the name of "gen-pairs" could be changed to something like
"gen-pair-parameters", because "gen-pairs" implies that the actual list of
pairs is being generated.

- 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 10:40 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] 1-4 interactions in a small molecule are missing

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
> >
> >
> >
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