that is the correct way to change inititial velocity distribution. you could
do a short run with ntwv=1 if you want to know the velocities.
ig sets the random number generator to different initial positions
On Sat, Dec 26, 2009 at 1:02 AM, balaji nagarajan
<balaji_sethu.hotmail.com>wrote:
>
> 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 Sat Dec 26 2009 - 05:30:03 PST
