[gmx-users] (no subject)

[Rishikesh Parulekar]

Thank you very much Justin Sir.


On Fri, May 6, 2016 at 4:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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