[gmx-users] Error in system_inflate.gro coordinates does not match

Justin Lemkul jalemkul at vt.edu
Thu Jul 17 12:16:27 CEST 2014

On 7/17/14, 4:52 AM, RINU KHATTRI wrote:
> hello gromacs users
> i used vmd and both the command pbc box and periodic images in all 6 frames
> +X -X +Y -Y +Z -Z and self but this action can not put protein inside the
> box
> and pbc box action only a box is created around protein and lipid 1/4
> protein is in side the box

All of this simply suggests that you built the system wrong, either by placing 
the protein in the wrong location with respect to the membrane and/or setting 
the box size too small for the system at hand, such that the protein "jumps" 
across a boundary.  As Dallas requested, it would be extremely helpful if you 
posted some images of what's going on.



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


More information about the gromacs.org_gmx-users mailing list