Re: Membrane Protein Simulation Problems

From: L. Michel Espinoza-Fonseca (
Date: Sat Oct 13 2007 - 11:01:02 CDT

> > My understanding from the previous email is that 27 has the CMAP corrections
> > as well.
> 22 and 27 do not include CMAP, which was released with 31. However, the
> labeling is quite confusing and I see that you seem to be using the right
> parameter file (which is labeled 27 and includes CMAP!?). Check the number
> of CROSSTERMS in your log file (STRUCTURE SUMMARY section) to be sure
> that you are using CMAP.

Just a single comment:

CHARMM 27 *does* include the CMAP correction. When using this version
of the ff, your NAMD log file shows that you have "x" number of
crossterms. I've been using the CHARMM 27 ff for the stability of
helices and you can indeed see the difference in terms of stability.
In fact, the paper by Buck et al. mentions such correction as

> >
> > "reinitvels" must not be working because I do not assign a temperature, thus
> > it would not know what distribution to select from. I have since removed
> > this option. Not even sure how it got into my script.
> Indeed, you are not using the "temperature" command, but your posted
> configuration files has a "set temperature 310" command and
> a "reinitvels" command (the command does work and you were overriding
> velocities in that particular case; note the subtle difference between
> the TCL variable temperature and the NAMD command temperature).
> >
> > Temperature averages out to 310K. The PME grid is 128x128x128.
> What is the size of the simulation box?? Is there enough space between
> periodic images?
> > 1.4 A resolution.
> Is the whole protein or a particular zone getting deformed? you may
> want to compute RMSD for some zones of the protein or compute RMSD per
> residue and check what part of the protein is behaving badly. By the
> way, when you said that your RMSD was going up, how bad is it? 2, 3, 6 A?
> I would also suggest to look at protonation states carefully (as suggested
> by Richard).
> > Hope that helps,
> >> Marcos

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