[gmx-users] refcoord-scaling

Justin Lemkul jalemkul at vt.edu
Tue Mar 25 02:24:10 CET 2014

On 3/24/14, 9:05 PM, Chetan Mahajan wrote:
> Hi Justin,
> My system is TiO2 crystal (2160 atoms position restrained) solvated by 3656
> water molecules, 1 formate anion and 1 sodium ion.  Is it true that when
> 'all' option is used, positions of the atoms (meant to be restrained)
> always change?

Consider what position restraints are doing.  They never guarantee that atoms 
won't move; they just apply a biasing potential to disfavor movement.  So yes, 
your atoms will probably move.  The smaller the system, the larger the effect 
will likely be.  Consider also what reference coordinates are doing.  They 
define how strong the potential is (distance between current coordinates and 
reference).  If you're scaling all atoms individually according to the pressure 
coupling, the reference moves and therefore the atoms can also move.  For larger 
systems like proteins, "refcoord_scaling = com" is normal and stable, and 
"refcoord_scaling = all" is disfavored.  Honestly, I don't know what to expect 
for a very small system like yours, but it is likely to be affected to a greater 

If the "all" option gives you a stable simulation that allow for proper 
equilibration, then I doubt there is any real problem.



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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