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

[Eric Smoll]

Hello Mark,

I did not answer one of your questions. You asked "what is the alchemical
state at 1.0?" The transformation involves lengthening the hydrocarbon
substituent of an organic molecule. At lambda=0.0, we have the short-chain
state. At lambda=1.0, we have the long-chain state. Since lambda=1.0
corresponds to a larger molecule, the overlap issue you describe is
possible. However, I can visualize the initial state of the total system
(atoms and dummies) to ensure that there is no problematic overlap and (as
far as I can tell) there is no overlap).

Another interesting note is that the problem atom-pair indices reported in
the error are different if small changes in the topology and mdp-settings
are made. This suggests that there is something fundamentally wrong with my
topology. However, the simulations run fine for all other lambda values
from lambda=0.0 to lambda=0.9 with the same topology/input-structure/mdp
settings.

Best,
Eric

On Thu, Apr 13, 2017 at 6:04 PM, Eric Smoll <ericsmoll at gmail.com> wrote:

> 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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