[gmx-users] how to repeat simulation correctly?

Albert mailmd2011 at gmail.com
Wed Nov 21 08:12:58 CET 2012


   I am quite confused on how to repeat our MD in Gromacs. If we started 
from the same equilibrated .gro file with "gen_vel        = no" in 
md.mdp, we may get "exactly" the same results which cannot be treated as 
reasonable repeated running. However, if we use "gen_vel=yes" for each 
round of running, sometimes our simulation may not converged at our 
simulated time scale and we may get two results with large differences.

   So I am just wondering how to perform repeated MD in Gromacs in a 
correct way so that our results can be acceptably repeated?

thank you very much.

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