Fw: [gmx-users] water molecule can not be settled
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540)
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