[gmx-users] friction constant for free energy calculation
jalemkul at vt.edu
Thu Feb 7 19:49:18 CET 2019
On 2/6/19 7:28 AM, minky son wrote:
> Dear gmx users,
> I was trying to calculate free energy.
> I’m confused about setting the appropriate value for friction constant (=
> In gmx manual, a value of 0.5 ps-1 (tau-t = 2.0 ps) was suggested
> but 1.0 ps-1 (tau-t = 1.0 ps) was used in Justin’s tutorial.
I was reproducing a published paper, so I used the same value. The
manual is not an authoritative source of "do this all the time," though
there are default or example values that are usually functional.
IIRC, when using sd, tau-t is read directly as ps^-1 and not inverted.
You'd have to check the code to be sure.
> How much the results are different by the use of tau-t value 1.0 or 2.0
Likely very little. The friction coefficient affects dynamics, but not
Justin A. Lemkul, Ph.D.
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