[gmx-users] (no subject)

[Justin Lemkul]

On 5/6/16 3:32 AM, Rishikesh Parulekar wrote:
> Hi,
>
>  I have completed simulation for 10ns and while analysing the trajectories
> through UCSF chimera i encountered that for some time my protein structure
> is getting distorted (pulled to other side from original confromation).
> Because of this I am getting fluctuated RMSD. My input parameters for
> md.mdp are same as mentioned in the bevan lab tutorial.  What could be the
> possible reason ??
>

With Google you would have gotten an answer in seconds, rather than hours...

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

-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

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