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
>>
>>_________________________________________________________________
>>FREE pop-up blocking with the new MSN Toolbar - get it now!
>>http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/
>>
>>-----------------------------------------------------------------------
>>The AMBER Mail Reflector
>>To post, send mail to amber_at_scripps.edu
>>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu