[gmx-users] About Shake and Lincs Algorithm

[vidhya sankar]

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
Thanks In advance
With Regards
S.Vidhyasankar