[gmx-users] D-L conversion!

[Anton Feenstra]

Swetha Vijayakrishan wrote:
> hi all,
> 
> I had run a 2 nanosecond MD using Charmm.
> Now i find a few of the residues having their chirality changed from L to
> D especially the Prolines.
> Is this very common in MD? Or have i made some mistake.
> Does anybody know how i can rectify this problem without rerunning the MD
> again??

One could argue whether doing MD with Charmm is a mistake ;-)

I would not expect L-D transitions in Prolines, these are known to be very
slow (experimentally, that is) and can be e.g. rate limiting for folding.
Don't know about the parameterization of the Charmm forcefield, however.

As for re-running, I know from other people that Charmm can be about 10
times slower than Amber, and I know from own experience that Gromacs can
be about 5-10 times faster than Amber. You do the maths...
We have a choice variety of forcefields: Gromos, OPLS (and Amber coming).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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