AMBER Archive (2005)

Subject: Re: AMBER: Velocity Info

From: Vineet Pande (pande_vineet_at_hotmail.com)
Date: Wed Mar 16 2005 - 10:02:04 CST


Thanks Guanglei..
In any case if its a restrt file from a relaxation (MD), where do I find
velocity info, what are the dimensions (units) of this velocity ......
Cheers
V
>
>Hi, Vineet,
>
>If you mean minimization (imin = 1), then you won't have velocities
>information in your restrt file. If you mean relaxation, then the velocity
>information can be read with irest = 1 and ntx = 7.
>
>Guanglei
>
>Vineet Pande wrote:
>>Dear Amber users:
>>I would like to know where is the velocity information written in the (-r
>>restrt) file, and what are its units...thats just for curiosity.
>>But..imagine I run a short MD with high restraints on solute (i.e. just
>>solvent MD) , and then I (just) minimize the solute gradually....do the
>>output coordinates (-r type) of these minimized files have velocity info.?
>>Do velocities change when minimizing things in NPT ensemble? This is
>>because then I need to do equilibration and I might use ntx=7, to read
>>velocities from previous runs...
>>
>>Thanks,
>>Vineet
>>
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