[gmx-users] FW: protein split over boundary
tsjerkw at gmail.com
Fri Apr 1 10:59:19 CEST 2011
On Fri, Apr 1, 2011 at 10:53 AM, anahita <ana_j0000 at yahoo.com> wrote:
> From: anahita [mailto:ana_j0000 at yahoo.com]
> Sent: Friday, April 01, 2011 1:13 PM
> To: 'gmx-users-request at gromacs.org'
> Subject: protein split over boundary
> Dear user,
> Hello, I appreciate if somebody help me. During the simulation of my protein
> I didn’t get any error but after 1ns of MD
> my molecule was split over boundary in cubic box. it means some part of it
> enter the other side of the box.
> At first,For decreasing the cost of simulation, in “editconf” command I set
> the number “d” on 0.9 to decease the box size. I want to mention that
> during the calculation my rvdw is 1.4.
> I want to know instead of problem of visualization, the other things is
> Best regards.
> A. johari
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Tsjerk A. Wassenaar, Ph.D.
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
More information about the gromacs.org_gmx-users