[gmx-users] mdrun error

[Justin Lemkul]

On 3/29/17 11:49 AM, amitbehra at chemeng.iisc.ernet.in wrote:
> Hello,
> After equilibrating my system for 100 ns( during which there was restraint
> on the protein letting the lipids to equilibrate), when I am trying to run
> my unrestrained run I am getting the following errors:
> 1. "bonds that rotated more than 30 degree"
> 2. "1 particles communicated to PME rank 0 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x"
> 3. "Listed nonbonded interaction between particles 71916 and 71920
> at distance 5.535 which is larger than the table limit 2.215 nm."
>
> What might be the reason for this error. I thought 100ns is enough for
> equilibration.
>

Something is likely topologically unsound.  The restraints were probably masking 
an underlying issue (100 ns is way longer than one normally runs for restrained 
dynamics, FWIW).

-Justin

-- 
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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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