[gmx-users] Request for dihedral PMF test system or complete alanine dipeptide topology file

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Jul 8 10:51:47 CEST 2007

This is not a question.

Previously I posted under this title when I was having difficulty  
reproducing alanine dipeptide 2D PMFs for Phi/Psi.

Update: Literature results have been reproduced. My entire problem was  
based on having a cis peptide bond for the C-terminal peptide bond in  
ALA. After constructing my initial state using pymol, I didn't pay  
enough attention to the impropers. After fixing that, everything is as  
it should be.

The point of posting this is twofold:
1) I said I would post when I solved the problem.
2) as a reminder to others that this is a good thing to check.

Embarassing? Yes.

A shout out to David Mobly and Vojt?ch Spiwok (on-list) and Jay ponder  
(off-list) who were very helpfull.

My original post:

dihedral alanine dipeptide potential of mean force error incorrect  
peptide bond large barrier high barrier

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