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

[Eric Smoll]

Hi Mark,

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

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. 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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