AMBER Archive (2003)

Subject: Re: AMBER: initial velocity

From: Peter Oelschlaeger (poe_at_caltech.edu)
Date: Fri Dec 19 2003 - 20:08:43 CST

Dear Fan,

yes, I think each atom is assigned a different initial velocity vector
depending on the random number seed. Maybe somebody knows more technical
details.
Multiple simulations are supposed to give better sampling than one long
simulation. See the Karplus paper Protein Sci (1998) 7:649.
In my experience the initial velocities have a significant impact on MD
simulations.
You can change the initial velocity by using differeng values for IG and
start at a temperature >0 K.
Hope this helps...

Peter

Fan Gao wrote:

>
>
> Dear Amber users,
> I have several questions for initial velocity in the MD simulation.
> I'm wondering if each atom has been assigned with a random initial
> direction and value of velocity in the starting frame? What is the
> advantage of running a series of short MD simulations with different
> starting frames compared with running a long MD simulation? How
> important is initial velocity for the MD simulation? How can we change
> the initial velocity for the simulation?
>
>
> Fan
> Fan Gao
>
> Receptor Biology Lab
> Medical Science Building 1-145
> Dept. of Physiology & Biomedical Engineering
> Mayo Clinic, College of Medicine
> Rochester, MN 55905
> USA
>
> Tel: 507-284-8461
> Fax: 507-284-9420
>
>
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-- 
**************************************************
Peter Oelschlaeger, Ph.D.
Mayo lab, Division of Biology, Caltech
1200 E. California Blvd., mail code 114-96
Pasadena, CA 91125-9600

Phone: 	(626) 395-8085, Lab: (626) 395-6407
Fax:	(626) 440-7231
Email:	poe_at_caltech.edu
http://www.mayo.caltech.edu
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