[gmx-users] Remove bad waters

Mark Abraham mark.j.abraham at gmail.com
Wed Apr 20 13:45:57 CEST 2016


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, 20 Apr 2016 13:40 Mehrnoosh Hazrati <mehrnoosh.hazrati at modares.ac.ir>

> 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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