[gmx-users] Group vs Verlet pair-lists
leilasalimi at gmail.com
Wed Jul 16 20:46:37 CEST 2014
On Wed, Jul 16, 2014 at 8:42 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
>> me what it is happened in Cut-off schemes = verlet?
>> And is it possible to have the trajectory with the right bonds (not broken
> This is a normal consequence of PBC and is not related to the cutoff
> scheme. Fix with trjconv -pbc mol or use VMD tools (
> 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
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users