[gmx-users] About Shake and Lincs Algorithm

[Justin Lemkul]

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

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

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

========================================