[gmx-users] refcoord-scaling

Justin Lemkul jalemkul at vt.edu
Tue Mar 25 01:39:03 CET 2014

On 3/24/14, 8:29 PM, Chetan Mahajan wrote:
> Thanks, Mark. So is 'all' option okay when positions of each of the atoms
> of TiO2 crystal (2160 atoms total) are restrained in space? Apparently, it
> does not seem correct, since positions of the atoms of TiO2 crystal change
> when 'all' option is applied. However, it does not give error as 'com'
> option does.

Is your system just a TiO2 crystal?  Is there any solvent?  If it's just a 
crystal, I see no point in restraining anything.  It is very unusual that the 
"all" option of refcoord-scaling is more stable than "com" - normally the 
opposite is true.  But that also explains why the coordinates are changing - the 
reference position of each individual atom is scaled according to the pressure 
coupling matrix, so the atoms are restrained to a dynamic reference, so it seems 
that it's not really accomplishing anything.



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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