From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Nov 17 2012 - 16:24:49 CST
I looked into this today. Stefan is using an outdated version of the CHARMM topology and parameters that do not have CMAP. The problem arises because when Mutator rebuilds the PSF file, it uses a more up-to-date version of the topology that adds some crossterms. When Stefan goes to the run the simulation with the outdated parameter file, it naturally can't find the appropriate values for those crossterms.
I will mention this to Stefan.
On Nov 16, 2012, at 1:48 PM, JC Gumbart 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?
>> Stefan Franzen: claims it does not
>> Anyone know for sure?
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