Re: membrane tutorial.

From: Francesco Oteri (
Date: Wed Sep 22 2010 - 03:24:58 CDT

Hi Swarna,
you need to push water to avoid the presence of water molecules within
the membrane.

Hi solved the problem without pushing water. I removed the waters
molecules with the following vmd command:

[atomselect top "not (same residue (z>10 and z <-10))"] writepsf memb.psf
[atomselect top "not (same residue (z>10 and z <-10))"] writepdb memb.pdb

In this way I've selected the water into the membrane basing on their z
position and saved a file without them.

On 22/09/2010 08:44, Swarna M Patra wrote:
> Hi Namd users,
> I am looking at the files of *Membrane Proteins Tutorial. I dont find
> a1b2c5_init.pdb can any one tell me what this file contains where I
> can get it. And how to select these water residue no in except water
> selection in keep_water_out.tcl script. I looked at the gramicidin
> tutorial also. why the lipid tail melt is done in gramacidin and also
> water push . is water push essential?
> thanks
> swarna
> *

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