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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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-requ...@gromacs.org.
