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
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