Re: Membrane Protein Simulation Problems

From: Marcos Sotomayor (
Date: Sat Oct 13 2007 - 10:36:06 CDT

On Sat, 13 Oct 2007, Ilya Chorny wrote:

> On 10/13/07, Marcos Sotomayor <> wrote:
> 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.

> "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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