Re: Accessing atoms and velocities during NVE run

From: Nd S (navdeep79_at_gmail.com)
Date: Fri Feb 06 2009 - 15:14:59 CST

Hey Cris

First of all thanks a lot for the quick response.

My problem is a carbon nanotube at the center of the cell surrounded by
liquid molecules. What I want to do is a constant heat flux simulation, by
constantly putting energy into the nanotube and removing the same amount
from the outside periphery of the cell. So for constant heat flux into the
nanotube, I am trying to get the velocities of the atoms of the nanotube and
rescale them depending on the calculations. Also by the same way, I will
rescale the velocities of the atoms on the periphery of the cell to remove
heat.

Also doing this simulation, I am not sure if I can use periodic Boundary
condition or not. Any help will be highly appreciated.

Thanks
Navdeep

On Fri, Feb 6, 2009 at 3:00 PM, Chris Harrison <char_at_ks.uiuc.edu> wrote:

> 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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