[gmx-users] Group vs Verlet pair-lists

[Justin Lemkul]

On 7/16/14, 2:21 PM, leila salimi wrote:
> Dear GROMACS Users,
>
> I have a question regarding the Neighbor searching, I used group scheme
> when I used 4.5 and now I found that there is verlet in version 4.6. When I
> compare the trajectories, For verlet simulation I found that the atoms of
> water molecules are separated and it caused the long bond in vmd. I mean
> that one hydrogen is located on the right side of the cell and the oxygen
> and another hydrgon are on the left side that the first hydrogen can come
> with periodic image, but these long bond (artifact bonds) are not
> convenient and it is difficult for visualization.
>
> I did not have this problem with previous method (group). Could you explain
> me what it is happened in  Cut-off schemes = verlet?
> And is it possible to have the trajectory with the right bonds (not broken
> bond)?
>

This is a normal consequence of PBC and is not related to the cutoff scheme. 
Fix with trjconv -pbc mol or use VMD tools 
(http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/23787.html).

-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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