[gmx-users] Remove bad waters

Mehrnoosh Hazrati mehrnoosh.hazrati at modares.ac.ir
Wed Apr 20 14:01:30 CEST 2016

Thank you dear Mark.

actually when I change my gro file by text and remove those water
molecules, I got "cannot settle water molecule" error, that I didn't get
using the first gro file.
So that I thought this way may not be appropriate!
Indeed, I don't get any error with those water molecules inside the
bilayer. But I'm afraid that's not be meaningful.



>This is easy to do in a text editor, because the z coordinates will stand
>out from the others. Make sure you also adjust the numbers of atoms and
>molecules accordingly. But a little bit of diffusion of water into the
>membrane can be physical (I think!) but too much suggests your model is
>broken somehow.


On Wed, Apr 20, 2016 at 4:09 PM, Mehrnoosh Hazrati <
mehrnoosh.hazrati at modares.ac.ir> wrote:

> hi all,
> I'm simulating membrane, and when I check my .gro file I found 4-5 water
> molecules got introduced into interstices in the membrane. I've changed
> vdwradii.dat file, but still these 4-5 molecules remain!
> Is there any way to delete them by VMD ?!  and if yes, how can I save the
> new file as .gro format?
> Thank you in advance
> Mehrnoosh

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