Dear Justin, Thank you very much from your help.
Oh, yes, the vectors of box are downward in the first with much slope and then the slope became milder and milder and then it become almost fix. For checking of density, should I use from formula: d=m/v? Best Regards Sara ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: mohammad agha <mra...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Thursday, October 4, 2012 7:01 PM Subject: Re: equilibrium for box of simulation Please keep the discussion on the gmx-users list. On 10/4/12 11:28 AM, mohammad agha wrote: > Dear Justin, > > Thank you very much from your help. > I don't know about "vectors trending downward, or do they converge" You can plot box vectors from the .edr file. That will give you their values and show trends in the data. > The change of density is from 1274 to 1685. and the slope of increasing the > density at the first is much and then it become almost fix. > This outcome suggests that your box likely has stabilized. You should still plot the vectors to understand what's going on. You also need to assess whether or not this density is acceptable as an evaluation of your physical model of the system. -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
