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

[Eric Smoll]

Good point. I only mutate one solute to a different solute. I do not have separate coulomb and vdw stages. If I examine the initial frame all atoms/dummies that undergo transformation are far from solvent molecule throwing the error. since the error is thrown on the first step I just don't see how it could be an overlap problem.

I have soft-core coul and VDW settings on. I assume they are applied to all atoms with B state parameters in the topology. how would I know if something is not being soft-cored properly?

Is there something else I can check?



> On Apr 13, 2017, at 5:54 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
> 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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