[gmx-users] refcoord_scaling

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 11 01:15:39 CEST 2012

On 7/10/12 5:48 PM, Katie Maerzke wrote:
> Hi all -
> I'm new to Gromacs (and MD).  I can't figure out whether or not
> refcoord_scaling is important for an NpT simulation.  In an MC simulation,
> when the volume changes, the coordinates of the molecules are also scaled.
> Does refcoord_scaling control how to handle scaling the molecular coordinates
> (e.g., scale all coordinates or scale based on COM), or does it do something
> else?  Is it even important?  I've searched the manual and the user forum,
> but I haven't found an answer to my question.

The important distinction is between reference coordinates and the actual 
coordinates of the atoms.  When employing position restraints, the restraint 
potential is based on the reference positions of the atoms.  It is these that 
are updated based on the refcoord_scaling option.  In most cases, the box 
shouldn't change drastically, and if it does, you have bigger problems.  Thus, I 
imagine the contribution to energy is likely small, but I have never tested this 
myself.  In theory, if the reference coordinates are not updated correctly, you 
will get incorrect contributions to the virial and thus some errors in pressure 

This is my understanding of the implementation; if it is incorrect or 
incomplete, hopefully someone will chime in.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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