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

Justin Lemkul jalemkul at vt.edu
Wed Jul 16 13:56:01 CEST 2014

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 but
> 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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