[gmx-users] refcoord_scaling = com

[Justin Lemkul]

On 6/14/13 2:58 AM, maggin wrote:
> at md stage,
>
> can we set refcoord_scaling = com  as follows,
>
> ; Pressure coupling is on
> pcoupl	 = Parrinello-Rahman	; Pressure coupling on in NPT
> pcoupltype	= isotropic	; uniform scaling of box vectors
> tau_p	 = 2.0	 ; time constant, in ps
> ref_p	 = 1.0	 ; reference pressure, in bar
> compressibility = 4.5e-5	; isothermal compressibility of water, bar^-1
> refcoord_scaling = com
>
> at lysozyme tutorial there is no  refcoord_scaling set.  I'm not sure if it
> could do that set refcoord_scaling = com at md stage
>

The refcoord_scaling option is only relevant when running an NPT ensemble with 
position restraints.  It is, in fact, used in the tutorial during NPT 
equilibration.  It is unnecessary during the other steps.

-Justin

-- 
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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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