Re: Using CHARMM-GUI membrane builder with NAMD

From: Bjoern Olausson (
Date: Mon Aug 02 2010 - 08:21:07 CDT

On Monday 02 August 2010 14:45:53 Axel Kohlmeyer wrote:
> > I would recommend reading about how CHARMM-GUI generates the membrane,
> > then some of your questions would vanish.
> >
> > Yes, water restraining makes in most cases no sense.
> >
> > Why do you want to keep the water out of something where it does not tend
> > to go voluntary? If at all, you should be concerned, that your water
> > does not
> this is true only if you have a well equilibrated system. the
> problem is that you have an unphysical vacuum when assembling
> the system. water molecules may go there due to the high
> potential energy from the assembling, but they may quickly
> get trapped. for the same reason, you want the lipid tails
> be restrained. even through that would eventually resolve
> itself, it will not happen during the timescale of typical simulations.
I agree 100%. In fact, I contradicted my own explanation of equilibration with
this statement.

> [....]
> > But I am not certain if this is really necessary since I never had
> > problems with water in the hydrophobic core. Even in self-assembly
> > studies there were no problems with water in the hydrophobic core.
> self-assembly is a different story, since the system stays
> close to equilibrium.
Right again.

Just to point out what I wanted to say:
Give it a try with just restraints to the heavy atoms and if it does not work
for you I guess your best shot is to either run the equilibration with CHARMM
or try with the "keep_water_out.tcl".


Bjoern Olausson
Martin-Luther-Universität Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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