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

Anirban reach.anirban.ghosh at gmail.com
Mon Apr 8 11:55:11 CEST 2013

I thought the sole purpose of open source discussions and sharing is to
help any scientific (or other) community to grow and benefit from each
other, without taking into account the Nationality of the beneficiaries. If
someone is willingly helping out somebody, whether Indian or not, in the
GROMACS forum, then it should not bother Mr. Luis Felipe Pineda de Castro,
since to the best of my knowledge it is not affecting him. I would request
the moderators of this forum to take adequate measures about such postings
as Mr. Castro's.



On Fri, Apr 5, 2013 at 10:55 PM, Luis Felipe Pineda de Castro <
luis.pinedadecastro at lnu.se> wrote:

> 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?
> 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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

More information about the gromacs.org_gmx-users mailing list