[gmx-users] energy minimization error

[Justin Lemkul]

On 5/16/15 11:35 PM, James Lord wrote:
> Hi Justin
> Thanks for this. Can you tell me which step(s) this bond length is defined????
> What should I do (redo) to resolve this issue?

The bonds are defined in the topology.  The DD algorithm reads what's in the 
coordinate file and builds cells based on the geometry it finds there.

Without a full description of what's in your system, what steps you've taken to 
prepare it (full commands, in order), there's little I can suggest because it 
would all be guesswork.

-Justin

-- 
==================================================

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

==================================================