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-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Shima Arasteh [shima_arasteh2...@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 <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@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_arasteh2...@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@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
