[gmx-users] Remove bad waters

[Mark Abraham]

Hi,

If you've done that properly, then you will have some holes in your
membrane and will need to re-equilibrate, e.g. Doing EM and theN perhaps
using a small time step while the local unhappiness resolves gently.

Mark

On Wed, 20 Apr 2016 14:01 Mehrnoosh Hazrati <mehrnoosh.hazrati at modares.ac.ir>
wrote:

> 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.
>
> Best,
> Mehrnoosh
>
>
> >Hi,
>
> >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.
>
> >Mark
>
> 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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