[gmx-users] Long bond streches during simulations

[Justin Lemkul]

On 10/29/14 6:21 AM, Seera Suryanarayana wrote:
> Dear gromacs users
>
> I have done mdrun upto 50ns by using the command "gmx mdrun -deffnm md_0_1
> -nt 7.
> I have total 8 threads  and I used 7 out of it along with graphic card
> nvidia tesla 2075.
>
> I first thing I would like to know that when I load the .trr or .xtc file
> after the .gro file into the vmd  some bonds stretched very long are being
> appeared parallel and vertical in red and white color. My question here is
> "Appearing  long bond stretches  while loading into vmd right or wrong?"
>
> At the end of the simulation my protein moves towards the side of the box.
> After some time (frame no. 1564)  few residues moves away from protein and
> some bonds stretched very long being appeared between that residues and
> rest of protein.
>
> Then the bond stretches  disappear from the frame number 1900 and again the
> bond stretch  being appeared during  rest of the simulation and at the end
> I got the final trajectory with some long bond stretching between some
> residues those moved away from the protein and the rest of the protein.
>
> Kindly inform me what could be the reason for the long bond stretching?
>

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

-Justin

-- 
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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

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