AMBER Archive (2003)

Subject: Re: initial velocity

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri May 02 2003 - 09:20:09 CDT

The ay I look at it, random velocities
are to be used when you _don't_ have
a restart file. This could be from a minimized
struccture, or something from Leap, or
a snapshot extracted from a trajectory file.
If I have velocities, I usually use them.

carlos

----- Original Message -----
From: "Youyi Peng" <pengyo_at_UMDNJ.EDU>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Friday, May 02, 2003 10:22 AM
Subject: initial velocity

> Dear AMBER fans:
> I have a question about the MD initial velocity. There are two ways to
> generate the initial velocity: one to use random velocity seed, the
> other to read from the restart file. I am not sure when to use the
> velocity information from the restart file. Does the initial velocity
> affect the MD very much? Personally I think the initial velocity
> shouldn't impact the MD very much for s table system. Would you please
> give me some advice how to choose the initial velocity?
> Thank you very much.
> Youyi Peng
>
>