[gmx-users] Remove bad waters
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
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
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users