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

[Shima Arasteh]

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? 


 
Sincerely,
Shima


________________________________
 From: Justin Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, April 5, 2013 7:42 PM
Subject: Re: Fw: [gmx-users] water molecule can not be settled
 






On Fri, Apr 5, 2013 at 10:27 AM, Shima Arasteh <shima_arasteh2001 at yahoo.com> wrote:

I' d like to know if it is acceptable to change the molecule coordinates to solve this problem?
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It's unlikely that some ad hoc change will magically fix a problem.  Energy minimization should take care of clashes.
 
Some time back, I deleted such a molecule and then I got a fatal error containing that the trj file and other inputs are not inconsistent.
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Right, because you've now changed the contents of the system.  It no longer matches the topology and the trajectory would then be discontinuous.

-Justin
-- 

======================================== Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
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