[gmx-users] Fwd: Broken chain / fragmentation

[Justin Lemkul]

On 5/27/17 9:42 AM, Tasneem Kausar wrote:
> Try -pbc whole

And for a more complete explanation:

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

-Justin

> 
> On 27 May 2017 18:09, "Biplab Ghosh" <ghosh.biplab at gmail.com> wrote:
> 
>> Dear Gromacs users,
>>
>> My Gromacs simulation on a protein terminated without any error and major
>> warning. However, when I see the conformations, I found them broken.
>>
>> For trajectory conversion, I have used the following commands:
>>
>> gmx trjconv -s protein-md.tpr -f protein-md.xtc -center -pbc nojump -ur
>> compact  -o protein-md-center.xtc
>>
>> gmx trjconv -s protein-md.tpr -f protein-md-center.xtc -fit rot+trans -o
>> protein-md-center-fit.xtc
>>
>>
>>
>> I would appreciate any help in figuring out where I am going wrong.
>>
>> Thank you all
>> Biplab.
>> --
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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

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