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

[Shima Arasteh]

You mean start over the NPT step?


 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
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

-- 

========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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