[gmx-users] Periodic Boundary removal in Coarse Grains Simulations

[Justin Lemkul]

On 2/22/14, 12:43 PM, Nikhil Agrawal wrote:
> Hi All,
>
> I have simulated a membrane proteins system using coarse grain model. after
> simulations when i removed periodic boundary from my simulations box but
>   the protein is moving up and down in the box ?  I have tried all the
> options nojump ,mol,whole ...etc. no options seems to work.
>

Without the exact sequence of commands, it's not possible to suggest where you 
might have gone wrong.  Note that multiple passes to trjconv are typically 
necessary.

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

> there is something wrong with my trajectory or it is normal with CG ?
>

Periodicity effects do not depend on the force field.  It is certainly possible 
that your box is too small for the system being considered, thus the PBC 
algorithms in trjconv can't reconcile things (and in that case, your trajectory 
would suffer from minimum image violations).  What are the dimensions of your 
box, and how much space exists between the protein and the box edges?

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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