[gmx-users] Error at FEP lambda = 1; seg. fault. with "larger than the table limit" message

[Mark Abraham]

Hi,

On Fri, Apr 14, 2017 at 1:49 AM Eric Smoll <ericsmoll at gmail.com> wrote:

> Hi Mark,
>
> Thanks for the rapid reply! I am using version 5.1.2. I can reproduce the
> error with 2016.1.
>

OK, that is useful to know.


> Note that "particles" (I assume atom indices counting from 1) 541 and 554
> do not correspond to the alchemical system, but to a dihedral or pair in a
> solvent molecule. So there should be no particle overlap issue.


Why couldn't one of the solvent atoms have overlapped with an eliminated
particle in the solute, and then gone flying? What is the alchemical state
at 1.0? Are there particles needing soft coring that perhaps aren't?

Mark

That being
> said, I am using VDW and coulomb soft-core settings.
>
> Best,
> Eric
>
>
> On Thu, Apr 13, 2017 at 5:40 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > On Fri, Apr 14, 2017 at 1:30 AM Eric Smoll <ericsmoll at gmail.com> wrote:
> >
> > > Hello GROMACS users,
> > >
> > > I am running NVT alchemical free energy simulations (change in atom
> > number,
> > > bonding, etc.). These simulations appear to go well at all lambda
> values
> > > below 1.0. At lambda=1.0, the system returns an error before or during
> > the
> > > first step:
> > >
> > > WARNING: Listed nonbonded interaction between particles 541 and 554
> > > at distance 183739120.000 which is larger than the table limit 5.500
> nm.
> > >
> >
> > On face value, some force went enormous last step to produce a ridiculous
> > distance here. To what alchemical state does lambda = 1.0 correspond? Can
> > this be some kind of overlap of two particles that e.g. should have been
> > soft-cored?
> >
> > However the same system (input structure + topology + mdp-settings) will
> > > minimize without any issue at same lambda=1.0 setting.
> >
> >
> > Doesn't really mean anything.
> >
> > What GROMACS version is this? Some more recent versions have some more
> > checks for things having gone crazy before this error would trigger. Can
> > you reproduce this with 2016.3?
> >
> > Mark
> >
> >
> > > I am not sure what
> > > is going wrong.
> > >
> > > Best,
> > > Eric
> > > --
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