[gmx-users] About Shake and Lincs Algorithm
jalemkul at vt.edu
Tue Aug 7 23:07:46 CEST 2012
On 8/7/12 9:17 AM, vidhya sankar wrote:
> Dear Justin ,
> Thank you for your Previous useful reply
> I Have used the Lincs Alogrithim for NPT Equlibration MD. But For Main MD I would like to use Shake Algorithim With Shake _tol = 0.00001 with continuation = yes
> Is it Correct to use two algorithm for simulation of same system (NPT, longMD)
> To which extent Will it Affect the result (Free energy)? Because I am doing Free energy calculation Based on Essential Dynamics ? Is it possible
I'm not prepared to predict such things. Whatever conditions you choose,
equilibrate sufficiently before collecting data. Switching algorithms and
immediately collecting data rarely, if ever, makes sense.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users