Re: How to create repulsive particle ?

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Nov 21 2006 - 16:05:18 CST

(or, import smthg.so, for those of us who can spell)

Peter Freddolino wrote:
> I've never done this myself, but I do believe this should work fine
> (although you might actually be looking for
> impost smthg.so
> )
>
> If all you want to do is use some C/C++ routines, you can also use the
> extforces command instead of Tclforces, which will dump coordinates to a
> file at specified time intervals, run an external program on them, and
> read the resulting forces back into NAMD.
>
> Please note, however, that both tclforces and extforces will only run on
> the head node, and thus you're likely to suffer greatly if you're
> expecting to scale to many processors... if that's the case, only
> tweaking the NAMD internals is really going to work well.
>
> Peter
>
> Arturas Ziemys wrote:
>
>> Thanks for answer !
>>
>> One more general question: Is it possible to import into Tcl Forces some precompiled and wrapped, say C/C++, library to skip slow Tcl numerical calculations ?
>>
>> And, if YES, is it sufficient to put the like like "import <smthg>" ? There that library should be saved (folder)? Should it be written right after the starting Tcl script:
>>
>> tclForcesScript {
>>
>> import <smthg>
>>
>> ...
>>
>> }
>>
>>
>> Best
>> Arturas
>>
>>
>>
>>
>>
>>> Hi Arturas,
>>> as far as I know this is not possible without editing the NAMD energy
>>> function (found in ComputeNonbondedBase2.h), although hopefully future
>>> versions will make this easier.
>>> Peter
>>>
>>> Arturas Ziemys wrote:
>>>
>>>
>>>> Hi,
>>>>
>>>> I am searching ways to introduce the particle which has only repulsive force and the repulsion is applied to some set or types of atoms: the rest atoms are "transparent" to the repulsive forces of that particle.
>>>>
>>>> Is there any way to implement that without Tcl forces in NAMD ?
>>>>
>>>> References to some similar implementations would be welcome.
>>>>
>>>> Best
>>>> Arturas
>>>>
>>>>
>>>>
>>>>
>>>>
>>
>>

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