Re: how to set initial velocity?

From: uu zhu (uuzhuzhu_at_gmail.com)
Date: Wed Apr 29 2009 - 01:58:13 CDT

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

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