Re: Using CHARMM-GUI membrane builder with NAMD

From: Ajasja Ljubetič (
Date: Mon Aug 02 2010 - 07:59:54 CDT

> I would recommend reading about how CHARMM-GUI generates the membrane, then
> some of your questions would vanish.

I confess I have only looked through the video tutorial and some basic
texts, but I did know it uses either a preequilibrated membrane or a library
of pre-equilibrated lipids (insertion or replacement method). I'm reading
through this <> and

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
> penetrate the membrane headgroups enough so you get a proper hydratisation.
> Equilibrations means that your system relaxes and eliminates vacuum
> regions.
> Either by moving structures or diffusing water. Restraints during
> equilibration is commonly used to prevent a deformation of your protein (or
> whatever Structure) because of to rapid heating, vacuum bubbles, bad
> hydratisation, etc.

These are my thoughts exactly - water doesn't want to go into the membrane
anyway. But in the Membrane protein
script is used to keep water out anyway. The only reason I could think of
for this is: during the insertion of protein in the
membrane inevitably some vacuum cavities are formed. Since water diffuses
faster than lipids it might fill this cavities before the lipid tails. But
if one allows the tails to equilibrate first it should not be a problem [I'm
taking too long to respond:) As Dr. Kohlmeyer pointed out, water can get

> The system generated by CHARMM-GUI uses equilibrated water boxes in which
> your
> structure is place. All water molecules which heavy atoms are closer then X
> ngstrm to your structure are removed. Same (more or less) is done with
> the
> lipids. Again the lipid coordinates are taken from a pre-equilibrated
> library.
> For the area/lipid some initial values are used. All these starting values
> are
> not optimal and in some cases introduce a lot of potential energy. So this
> is
> what you want to overcome in an equilibration and the restraining helps to
> keep your structures in shape in case they suffer from effects I mentioned
> above.
> So just restrain the heavy atoms of your DNA backbone and if you want the
> heavy atoms of the lipid head groups (If you really want, put some low
> forces
> on the heavy Atoms of the lipid tails).
> In most cases it is not even necessary to slowly heat (even less necessary
> when you use restraints and slowly remove them as I suggested in my
> previous
> post)
You are right, I'll try this first and if something goes wrong I'll know in
a day or two and can always rerun the equilibration.

In fact the CHARMM GUI restraints the water molecules:
> define twater sele ( resname TIP3 .and. type OH2 .and. .not. ( segid PWAT
> .or.
> segid WAT* ) ) end
> GEO plane -
> xref 0.0 yref 0.0 zref 0.0 zdir 1.0 -
> harmonic outside force @wforce droff 11.0 select twater end
> It restrains the lipids as well, but the script is a bit more complex (I
understand the water part, but for the lipids it restrains
the head-groups as well as the orientation of the tails). For example I have
to look up what GEO plane RCM is -
aha<>it's a
restrained on the center of mass .

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.
Thank you very much for your answers.
Best regards,

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