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

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Apr 5 17:19:03 CEST 2013

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? 


 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?

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.

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

More information about the gromacs.org_gmx-users mailing list