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
--
========================================
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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