Re: Accessing atoms and velocities during NVE run

From: Nd S (navdeep79_at_gmail.com)
Date: Fri Feb 06 2009 - 13:33:53 CST

Hi Cris

My problem is first I need the velocities to calculate the temperature and
then use that temperature as a reference to modulate the velocities.

Navdeep

On Fri, Feb 6, 2009 at 12:06 PM, Chris Harrison <char_at_ks.uiuc.edu> wrote:

> Navdeep,
>
> You can use tclforces and a "tclforces script" (which you will have to
> write) to acquire the coordinates at each step and apply a force to the
> atom(s) to modulate the velocity.
>
>
> C.
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>
>
>
>
> On Fri, Feb 6, 2009 at 10:57 AM, Nd S <navdeep79_at_gmail.com> wrote:
>
>> Dear NAMD users
>>
>> I am running a NVE simualtion and after each step I want to modify the
>> velocities of of atoms a certain distance apart from the center of the
>> cell. How can I access the velocities and co-ordinates of the atoms after
>> each step run and modify them.
>>
>> Thanks
>> Navdeep
>>
>
>

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