Re: Accessing atoms and velocities during NVE run

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Fri Feb 06 2009 - 15:00:36 CST

Navdeep,

At present there is not a direct way for a user to directly get and
instantaneously modify the velocities on the fly. You could try to
effectively do this by:

1. writing a tclforces script that tracks coordinates, calculates the
effective velocities, and effectively modifies the velocities by applying an
artificial force.

2. Write a script that runs namd 1 timestep, gets the velocities from the
dcd, performs the calculation you want to yield modified velocities for the
atoms, and then re-run namd restarting from the previous run's coordinates
but inputing the modified velocities.

A third option would be to hack the code but you'd be messing with code very
close to the core so frankly I would be rather skeptical of results without
sufficient evidence.

Artificially modifying the velocity on the fly within a timestep will
displace your system from it's current energy surface to a new energy
surface, breaking your ensemble so I'm not sure why you really want to do
this.

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 1:33 PM, Nd S <navdeep79_at_gmail.com> wrote:
> 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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