[gmx-users] Something weird with shell particle dynamics

[Justin Lemkul]

On 6/15/16 5:06 AM, Luca Banetta wrote:
> Dear all gromacs users,
>
> I am trying to run a shell molecular dynamics simulation using  GROMACS
> version 4.6.5.
>
> First of all a shell particle has been introduced in an OPLS-AA force field.
>
> Unfortunately, immediately after the mdrun has been started this fatal
> error appeared: “Something weird with shells. They may not been bonded to
> something”. I try to understand  the error  taking a look at the source
> code “shellfc.c”  but I don’t really imagine a possibile cause for this
> situation.
>
>
>
> Can someone suggest me a possible origin of this mistake?
>

Either the topology is wrong or your method of declaring the shell type is 
wrong.  Without seeing the modified force field file(s) and topology, it's 
impossible to say.

-Justin

> Really looking forward to hearing from anyone soon.
>
> Best regards.
>
> Luca
>
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-- 
==================================================

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

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