Dear Amber !
I would like to do the MD with different velocities for the same system .
with reference to amber manual IG is the tag determines the velocity by random seed selection ,
so, i tried it for the peptide having 5 residues using GB , with different ig values
like 71277 is the default for the first run and i gave the other two run having the same initial condition and changed the
ig value as 35000 and 0 respectively . accordingly i observed the variation in the potential energy
between these three simulations .
i would like to know , how the velocity is calculated from this random number
and what are the velocities for the values that i have fixed .
could any one tell me what are the other ways to change the velocities if i am not more specific .
thanks
regards
balaji
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Received on Fri Dec 25 2009 - 22:30:03 PST
