[gmx-users] pbc problem

[Justin Lemkul]

On 1/29/14, 9:13 AM, Atila Petrosian wrote:
> Dear Justin
>
> Thanks for your reply.
>
> To obtain modified trajectory and then comparing with original trajectory,
> I do not know exactly which of none, mol, res, atom, nojump, cluster or
> whole is appropriate for me.
>

In a simple case like this, many of the options may produce equivalent outcomes. 
  Explore the list archive a bit, because periodicity is discussed frequently. 
Also consult 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow 
and play around with trjconv - nothing supplants a bit of trial and error 
sometimes, especially with a Swiss army knife program like trjconv.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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