Re: change force field in NAMD

From: Erik Santiso (
Date: Fri Oct 22 2010 - 11:05:50 CDT


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.



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:
> 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.
> I found the one below particularly useful, although it is a bit old:
> 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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