Re: Using CHARMM-GUI membrane builder with NAMD

From: Axel Kohlmeyer (
Date: Mon Aug 02 2010 - 07:45:53 CDT

> 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.


> 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.


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

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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