Re: change force field in NAMD

From: Erik Santiso (esantiso_at_mit.edu)
Date: Fri Oct 22 2010 - 11:05:50 CDT

Hi,

Do you just need to calculate/print those interactions as the simulation
goes on or modify them in some way? I suspect it would be pretty hard to
modify them.

I'm copying your question back to the mailing list, probably others can
give you additional advice on this.

Best,

Erik.

On 10/22/10 11:27 AM, Chen, Zhihong (chenz2) wrote:
> Hi ,Erik,
> Thanks for your helpful information. I thought NAMD would not let me do that. I need to partition the eletrostatic interaction into local and far-field energy, and do a sampling for each, and do the same for the vdw interaction. I am new to namd and not familiar with programing. can u give me some advice? Thanks
> regards,
> jackie
> _ _______________________________________
> From: Erik Santiso [esantiso_at_MIT.EDU]
> Sent: Friday, October 15, 2010 8:30 PM
> To: Chen, Zhihong (chenz2)
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: change force field in NAMD
>
> Hi,
>
> Unfortunately, it is not so simple - there isn't a single piece of code
> where NAMD calculates the forces. Depending on exactly what you want to
> change, it may be relatively simple or may require a major programming
> effort (which you may not want to carry out).
>
> The structure and inner workings of NAMD are described in several online
> documents, e.g.
>
> http://ftp.ks.uiuc.edu/Research/namd/development.html
>
> I found the one below particularly useful, although it is a bit old:
>
> http://www.ks.uiuc.edu/Research/namd/1.5/pg.ps
>
> Maybe you could be a bit more explicit about exactly what you want to
> change?
>
> Erik.
>
> On 10/15/10 10:50 AM, Chen, Zhihong (chenz2) wrote:
>>
>> Hi, all
>> I am interested in changing
>> the functional form of the force field equation in NAMD, as in add or
>> remove some terms from the eqn. But i am not sure if namd let me do that or not. I know that i may need to do some programming
>> and i'm willing to do that, so i would be very grateful if someone could
>> guide me abt how shld i got abt it. Which source file contains the code for
>> the eqn? And at what all levels i'll have to make the changes?
>> regards,
>> jackie
>>

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