Re: how to set initial velocity?

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Wed Apr 29 2009 - 15:09:34 CDT

According to the user's manual (http://www.ks.uiuc.edu/Research/namd/2.6/ug/node14.html
) you can specify velocities via a pdb file, using the "velocities"
keyword. It would make sense that you would just replace the position
fields with your select velocities. The pdb format is quite particular
about the spacing and syntax, so you'll have to be a little careful,
but the best thing to do is just try it out. My guess is that it
should work.

Josh

On Apr 28, 2009, at 11:58 PM, uu zhu wrote:

> Hi, Josh,
> Thanks for your email.
> Actually, I plan to set some special velocities for the initial
> state, and maybe it is better to write these parameters by hand in
> an external file. Do you know how to set for this case?
> Thanks.
> Best regards,
>
> On Wed, Apr 29, 2009 at 10:59 AM, Joshua Adelman <jadelman_at_berkeley.edu
> > wrote:
> 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
> ------------------------------------------------------------------------------------------------------
>
>
>
>
>
>
> --
> 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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