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

Mark Abraham mark.j.abraham at gmail.com
Fri Apr 14 01:40:56 CEST 2017


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

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?


> I am not sure what
> is going wrong.
> Best,
> Eric
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