From: Michelle Kuttel (mkuttel_at_cs.uct.ac.za)
Date: Wed Nov 23 2011 - 23:31:14 CST
Thanks for all the input on this so far.
> I was not aware that the implementation of the CHARMM force field in NAMD needed validation.
I think *everything* needs validation! Especially in simulation science. ;) I'm just making sure that everything works before I continue. This is a force field for carbs that I parameterized years ago in CHARMM and I'm retracing my original steps.
> And in any case, I would not take the final outcome of an iterative calculation as the test. I would directly compare all of the atomic forces at step 0 from the same identical structure, if I was worried that NAMD was not implementing the CHARMM ff accurately.
>
> "targetNumSteps" does not affect the force. Rather, the force you choose along with all the other options will affect the result. Also, because minimization will always fall to the nearest configuration, the initial structure matters a lot.
But it definitely does! It may not be clear from the discussion, but I can get the calculation to work (see options listed in previous email). However, it's when I specify more steps for minimization (or more stages) that I then need a higher force to get the same result. It is odd and it is bothering me.
>
> What structure did you start the calculation from? That is, what was the initial value of the dihedral?
>
> If you minimize the structures corresponding to the three minima you say, are these structures stable?
>
> If you compute a relaxed energy profile between two of these minima (rather than the full -180:180 range), what is the result?
>
I'll try this (the initial value is -60 degrees). However, in the interests of progress, I think that I will simply move to using the more sophisticated ABF free energy calc.
Thanks again.
Michelle.
---------------------------------------------
Michelle Kuttel
Department of Computer Science
University of Cape Town
Cape Town
South Africa
mkuttel_at_cs.uct.ac.za
PH: +27 21 6505107
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