From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Nov 16 2012 - 14:26:56 CST
You're really outthinking yourself here. Of course it's used properly for everything. See the tutorials, numerous papers, etc. for examples.
On Nov 16, 2012, at 1:51 PM, Dr. Eddie wrote:
> Is it only for the energy calculation? Is it not used in the dynamics then?
>
>
> On Fri, Nov 16, 2012 at 1:48 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> This line, for example, in the log file begs to differ:
>
> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
>
> CMAP has been in NAMD for many years now. This may be (or have been?) a mutator specific issue. If so, someone should check more closely that the plugin isn't generating additional superfluous cross terms.
>
> On Nov 16, 2012, at 1:15 PM, Dr. Eddie wrote:
>
>> does namd use the cross-terms in the psf file for its calculations or is it ignored?
>>
>> Prof.
>> Stefan Franzen: claims it does not
>> http://www4.ncsu.edu/~franzen/public_html/CH795N/projects/DHP_MD.htm
>>
>> Anyone know for sure?
>> Thanks,
>> Eddie
>>
>
>
>
>
> --
> Eddie
>
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