[gmx-users] Segmentation fault

Justin Lemkul jalemkul at vt.edu
Mon Aug 29 15:00:44 CEST 2016

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On 8/29/16 6:16 AM, Seera Suryanarayana wrote:
> Sub: Segmentation fault
> Dear Justin and Vivek,
> I came to know what was my fault. I added the refcoordscale = com  in .mdp
> file and it going fine. I have through the many references for
> refcoordscale, despite of some information I am not getting what exactly it
> is?  Kindly give me some hit.

The pressure coupling scaling matrix adjusts atomic positions in response to 
variations in pressure.  If you use a fixed reference as the origin of the 
position restraints, you will get a systematic drift in that position with 
respect to the coordinates propagated during dynamics.  So with the 
refcoord_scaling option, the reference coordinates (e.g. those at t=0, usually) 
have the same scaling matrix applied to them so that you don't get spurious 
contributions that might distort the structure.  The "com" option scales 
relative to the center-of-mass of the restrained group(s), whereas "all" scales 
every atom individually.  I find "com" to generally be the best option.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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