Re: how to set initial velocity?

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Tue Apr 28 2009 - 21:59:21 CDT

You probably do not want to set the initial velocities by hand in an
external file. It is best to use one of the methods detailed in the
user's guide:
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node30.html

My personal preference is using the Langevin thermostat to gradually
increase the temperature from 0 K to the desired temperature, although
this might not be best depending on your specific application.

Also be sure to check the namd-l archive as related topics have surely
been discussed in the past.

Best of luck.
Josh

On Apr 28, 2009, at 7:27 PM, uu zhu wrote:

> Hi, all
> These days, I plan to set initial velocity of some molecules after
> energy minimization.
> In the user's guide, it is mentioned that the initial velocity could
> be set in PDB file.
> However, I cannot find the PDB format for velocity.
> Does anyone know how to set that? Thanks.
> Best regards,
> --
> WANG
> PhD
> Division of Bioengineering
> School of Chemical & Biomedical Engineering
> Nanyang Technological University
> Singapore

------------------------------------------------------------------------------------------------------
Joshua L. Adelman
Biophysics Graduate Group Lab: 510.643.2159
218 Wellman Hall Fax: 510.642.7428
University of California, Berkeley http://nature.berkeley.edu/~jadelman
Berkeley, CA 94720 USA jadelman_at_berkeley.edu
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