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

Fri Apr 14 03:41:21 CEST 2017

Hello Justin,

Thank you for the reply! I just tested this. Although this solution does
not let me identify exactly where the bad contact is, selecting a new
starting structure alleviates the problem entirely.

Thank you for the help Justin and Mark!

Best,
Eric

On Thu, Apr 13, 2017 at 7:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/13/17 9:12 PM, Eric Smoll wrote:
>
>> 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.
>>
>>
> I wouldn't suggest running each lambda state from the same input
> structure; you would do better to run each sequentially so that the
> transformation is gradual and the solvent can relax around the transforming
> solvent as a function of lambda.  That will almost certainly alleviate any
> clashes that arise from an otherwise sudden change in the topology.
>
> -Justin
>
>
> 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
>>>>>>> --
>>>>>>> Gromacs Users mailing list
>>>>>>>
>>>>>>> * Please search the archive at
>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>>>> posting!
>>>>>>>
>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>
>>>>>>> * For (un)subscribe requests visit
>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>> or
>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>>> posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/
>>>>
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>