On 5/16/13 8:12 AM, gromacs query wrote:
Dear All,
I have a system with two solutes (A and B) with water and ions. For
pressure coupling in index file I defined two groups: Solute and Solvent,
where solute consists of A+B and solvent consists of water+ions
Due to some reasons I need to apply position restraints on Solute A only
for few ns NPT run then make it free also. So while doing NPT run and using
above said two groups in pressure coupling; that is Solute (A+B) and
Solvent (water+ions) I get this Warning:
You are using pressure coupling with absolute position restraints, this
will give artifacts. Use the refcoord_scaling option.
Should I ignore this warning or do any of following:
1) Defining two groups: One with Solute A only and Second group with
SoluteB+Water+ions
The error arises due to pressure coupling, not temperature coupling. I don't
think you necessarily need to split up the temperature coupling groups differently.
2) I am not sure which option I should use for refcoord_scaling option
In almost all cases, use the 'com' setting for refcoord_scaling.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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