Dear Justin,
Thank you very much from your response. This question was because of my previous problems about equilibration the box that I sent it with subject "equilibrium for box of simulation". When I equilibrate solvent and additives separated and then add to surfactant and after that equilibrate totally, there are not previous problems and I wanted to know that this method is correct? Best Regards Sara ________________________________ From: Justin Lemkul <jalem...@vt.edu> To: mohammad agha <mra...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Monday, October 15, 2012 5:21 PM Subject: Re: [gmx-users] about equilibrium On 10/15/12 8:56 AM, mohammad agha wrote: > > > Dear Gromacs Users, > > > > I have one system consists of: surfactant, solvent and additives. I made one > box with only solvent and one box with only additives and equilibrated them > little separable for better placing into the box, and then made one box with > surfactant and then placed box of solvent and additives (that before I had > equilibrated them separable) in the box of surfactant (by genbox) and > equilibrated it totally. > > May I know that this work is correct or not, Please? Maybe. It's hard to tell. Note that when you post the same thing four times and do not get a reply, it's usually due to the fact that it's hard for us to figure out what's going on. I don't know what your goal is but your approach is a bit hard to comprehend as written. One can usually build a multi-component system rather easily with a few invocations of genbox -ci -nmol, but then too, I don't know if you need some particular configuration (surfactant micelles?) or if random positions will suffice. Prior equilibration of solvent is probably a good approach. -Justin -- ======================================== 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 ======================================== -- 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
