Re: WCA Particle

From: Giovanni Bellesia (gbellesia_at_chem.ucsb.edu)
Date: Thu Jul 10 2008 - 16:07:25 CDT

Hi,
I just want to add a few words to what Peter said.
We've been using the tabulated potential code for quite a while. It's
stable and very easy to use.

Giovanni
> Hi Dave,
> if you're feeling adventurous, we have some tabulated potential code
> that does exactly what you describe (spline lookup table). I will send
> you the code off-list so you can try it out. It's still being shaken a
> bit more before being added to cvs.
>
> Best,
> Peter
>
> Dave Rogers wrote:
>> Dear NAMD gurus,
>>
>> I want to simulate a large protein system and include a
>> Weeks-Chandler-Anderson (WCA) particle. This would involve adding an
>> atom to my topology which interacts with other atoms using a shifted
>> LJ potential out to the minimum, at which point it becomes zero.
>> Gromacs has a "read pairwise potential from file" option that has
>> allowed me to do this in the past.
>>
>> I am thinking I might be able to do the same type of thing in NAMD
>> by creating a spline lookup table specifically for this
>> WCA-to-everything interaction, but how do I get NAMD to use this table
>> instead of the usual one? I have also considered using the tclforces
>> scripting interface, but this would require me to check all pairwise
>> distances inside of tcl -- which would by about as efficient as
>> writing my own MD code (unless I've overlooked something).
>>
>> What (if any) is the simplest -- i.e. least code modification -- way
>> you can imagine doing this and your estimated difficulty level (in Lt.
>> Scotty hours)?
>>
>> Thanks,
>> David M. Rogers
>> PhD Candidate
>> Dr. Beck Lab
>> University of Cincinnati
>>
>

-- 
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Giovanni Bellesia
Department of Chemistry and Biochemistry
University of California, Santa Barbara
Santa Barbara, California 93106-9510, USA.
Email: gbellesia_at_chem.ucsb.edu
Phone: 805 893 2767
Web: http://www.chem.ucsb.edu/~sheagroup/
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