[gmx-users] About Shake and Lincs Algorithm

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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