Re: WCA Particle

From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Wed Aug 06 2008 - 09:48:45 CDT

Sorry for my lateness in seeing this message.

I just wanted to ask if there was any effort in including tabulated bonds,
angles, or dihedral components in addition to the intermolecular part?

Thanks.

Josh

On Fri, Jul 11, 2008 at 5:07 AM, Giovanni Bellesia
<gbellesia_at_chem.ucsb.edu>wrote:

> 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
>>>
>>>
>>
>>
>
> --
> ------------------------------------------
> 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/
> ------------------------------------------
>
>

-- 
------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Dept. of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu
------------------------------------------------

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