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

Luis Felipe Pineda de Castro luis.pinedadecastro at lnu.se
Fri Apr 5 19:25:15 CEST 2013

After having followed for longer time the queries sent by some Indian fellows, I wonder if it wouldn't more effective to arrange for a GROMACS tutorial offered by Justin in an Indian location. Maybe you, the Indian fellows, can arrange for the financing and invite Justin to hold such a Tutorial on the  basics of MD simulations and their implementation in GROMACS. Considering the time Justin is spending responding to your queries, maybe because you are devoid of adequate supervision or theoretical background, this would be only fair. This posting is maybe a little bit off topic, but somehow related.

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Shima Arasteh [shima_arasteh2001 at yahoo.com]
Sent: Friday, April 05, 2013 5:22 PM
To: Discussion list for GROMACS users
Subject: Re: Fw: [gmx-users] water molecule can not be settled

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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