[gmx-users] Error in system_inflate.gro coordinates does not match
nickname.mittu at gmail.com
Thu Jul 17 10:52:11 CEST 2014
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
and pbc box action only a box is created around protein and lipid 1/4
protein is in side the box
how to put it in side
On Wed, Jul 16, 2014 at 5:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 7/16/14, 6:53 AM, RINU KHATTRI wrote:
>> hello gromacs users
>> i am working on protein complex with popc membrane
>> at the time of minimization and shrinking steps my protein complex is out
>> of the lipid membrane protein is in the lipid membrane till inflate.gro
>> after that it is out
> This indicates that the protein is not properly centered or the box is of
> insufficient size to accommodate the components of the system. Use "pbc
> box" in the Tcl console of VMD on the input and output structures and it
> should be obvious what is 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
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