Re: nitrogen in namd

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Jul 28 2011 - 11:57:05 CDT

There is no code in NAMD to constrain atoms along a line like this, so
you're going to need to define N-Na bond and N-Na-N angle spring constants
in the paramter file as well as shifting some mass from N to Na atoms.

-Jim

On Wed, 27 Jul 2011, Jeffrey Potoff wrote:

> This is pretty easy to do in NAMD. The topology looks like this:
>
> RESI N2 0.0
> GROUP
> ATOM N1 N -0.482
> ATOM N2 Na 0.984
> ATOM N3 N -0.482
> BOND N1 N2 N2 N3
> ANGLE N1 N2 N3
> PATCHING FIRS NONE LAST NONE
>
> You just need to create a dummy site with some mass and set the LJ parameters
> of 0.
> Jeff
>
> On 7/27/2011 3:49 PM, Erik Nordgren wrote:
>> Ciao Marco,
>>
>> I haven't done that sort of thing before, but it seems like you would just
>> need to create a little topology file that defines your 3-particle nitrogen
>> "molecule" as you describe, including the two "atom" types (one type with
>> mass~14, one with mass=0), and then add some lines to your force-field
>> parameter file (to impose a rigid 180-degree angle between the 3 particles,
>> for example). Have you tried anything like this already? If so, did you
>> encounter specific problems?
>>
>> Also, out of curiosity, wouldn't those charges be reversed, i.e., negative
>> partial charge in the middle and positive charge on the nuclei?
>>
>> -Erik
>>
>> --
>> C. Erik Nordgren, Ph.D.
>> Department of Chemistry
>> University of Pennsylvania
>>
>>
>> On Wed, Jul 27, 2011 at 5:47 AM, Marco Sant <labicia_at_yahoo.it
>> <mailto:labicia_at_yahoo.it>> wrote:
>>
>> Good morning,
>> I would like to compute the self-diffusion of N2 within a porous
>> material using namd.
>> I need to place a point charge on each N atom plus a point charge
>> in the center of mass of the N2 molecule. In other words, I need
>> something like a "virtual site" or a "dummy atom" having charge
>> but not mass and being placed in the center of the N2 molecule.
>> shape of N2
>> N---------N
>> (-) (+) (-)
>> Which is the best way to do this with NAMD?
>> Thanks a lot for the attention,
>> best regards,
>> M&B
>>
>>
>
>
> --
> ======================================================================
> Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
> Associate Professor Wayne State University
> Department of Chemical Engineering and Materials Science
> 5050 Anthony Wayne Dr Phone:(313)577-9357
> Detroit, MI 48202 Fax: (313)578-5815
> http://potoff1.eng.wayne.edu
> ======================================================================
>
>

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