Re: Membrane Protein Simulation Problems

From: Ilya Chorny (
Date: Sat Oct 13 2007 - 10:13:56 CDT

On 10/13/07, Marcos Sotomayor <> wrote:
> Hi Ilya,
> Looking at your previous e-mails, I would suggest the following:
> - Use the CHARMM31 force-field, which is the same as 22 and 27 for
> proteins but also includes the CMAP correction. The CMAP correction has
> been shown to stabilize RMSD and alpha-helices (see Buck et al, BiophysJ
> Letter, 90:L36-L38 2006). You will need to recreate your psf files.

My understanding from the previous email is that 27 has the CMAP corrections
as well.

- I wouldn't use the "zeromomentum" option when using constraints and/or
> Langevin dynamics, as in those cases the system *should not* conserve
> momentum (it is OK if the center of mass of the protein moves around a
> bit).


- Do not use the "reinitvels" command every time you restart a simulation,
> as you are reading the velocities from the previous run (in the conf file
> you posted before, you were basically reading the velocities from a
> previous run and then overriding them).

"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.

- Is your system neutral overall?


- Check your periodic boundary conditions, your temperature, the size
> of your PME grid.

Temperature averages out to 310K. The PME grid is 128x128x128.

- If your protein is a bad model, or of poor resolution, or somehow
> distorted by crystallographic artifacts, you may never get a good
> convergence on RMSD. Unfortunately MD will not refold your protein on a 10
> nanosecond time scale :-)

1.4 A resolution.



Hope that helps,
> Marcos
> On Fri, 12 Oct 2007, Ilya Chorny wrote:
> > Dear Richard,
> >
> > I got your contact info from the NAMD mailing list. I am a member of the
> > Stroud Lab at UC San Francisco and I am working on a membrane protein
> > simulation. I am having some trouble with my protein. I prepare my
> > simulation box by inserting the protein into the membrane, deleting
> > overlapping lipids, solvating the system and adding counter ions. I
> minimize
> > and then equilibrate the system for 2 ns. In the initial 2 ns simulation
> I
> > fix the position of protein atoms and constrain the lipid phosphates in
> the
> > Z dimension (along the pore axis). I then run an 8ns simulation in which
> I
> > release the constraints on the lipid and constrain the CA positions of
> the
> > protein. After my 10 ns equilibration I run another 8 ns simulation in
> which
> > the whole system is free. In the last 8 ns simulation my protein seems
> to be
> > falling apart. The RMSD keeps increasing and the channel residues which
> > should be fairly constrained move all over the place. I monitor my
> > equilibration by calculating the protein-lipid energy which seems to
> have
> > converged. Any ideas on what I can do to debug my problem? The
> membrane is
> > POPE.
> >
> >
> > Thanks,
> >
> > Ilya
> >

Ilya Chorny Ph.D.

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