Fw: [gmx-users] water molecule can not be settled

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Apr 5 17:22:36 CEST 2013

You mean start over the NPT step?


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Friday, April 5, 2013 7:50 PM
Subject: Re: Fw: [gmx-users] water molecule can not be settled

On Fri, Apr 5, 2013 at 11:19 AM, Shima Arasteh
<shima_arasteh2001 at yahoo.com>wrote:

> As I visualized the system, I see a water molecule somewhere between lipid
> chains near the protein entrance. This has been happen during NPT. I' d
> like to delete this molecule but with such a kind of fatal error this would
> impossible. So what's the way?  Is there any tricky way to change
> coordinate of molecule? but I seems also impossible becasue PME problem!
> So whats the solution?
Delete the molecule, adjust your topology (and index file, if necessary),
and start over with the equilibration.




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)

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