Hello Tsjerk and Justin, Thank you for the suggestions. I found the "suggested trjconv workflow" ( http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions) very helpful. I followed the workflow, including the "-pbc nojump" step and found success.
Thank you so much for your help. Best, Eric On Tue, Aug 26, 2014 at 1:49 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hey :) > > What about -pbc nojump -center ? > > Cheers, > > Tsjerk > > > On Tue, Aug 26, 2014 at 8:12 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 8/26/14, 12:30 PM, Eric Smoll wrote: > > > >> Hello GROMACS users, > >> > >> I have created an infinite liquid film system by building a slab of > >> molecules in a 3D periodic unit cell where two dimensions of the film (x > >> and y) extend out to the edge of the unit cell and one (z) does not. > >> > >> I found the slab drifts along the z-dimension during MD and I am trying > to > >> post-process the trajectories to anchor the slab in the center of the > unit > >> cell. > >> > >> "trjconv -pbc mol -center -boxcenter" works well for most trajectories > >> *unless* the slab drifts so much that it comes in contact with the z > >> boundary. When this occurs, "trjconv -pbc mol -center -boxcenter" > anchors > >> it in a different location. Any ideas how I can anchor the system to the > >> center of the unit cell in this situation? > >> > >> > > The -fit options should help here, either progressive or translation. > > > > -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. > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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. > -- 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.