This is a sample of energy minimization, solvation and ion neutralization in my own system ( protein in POPC):
Steepest Descents converged to Fmax < 100 in 18240 steps Potential Energy = -1.0357691e+06 Maximum force = 8.0741402e+01 on atom 4716 Norm of force = 3.1694601e+00 I think it seems sensible, however I am not sure. Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Thursday, October 11, 2012 2:21 PM Subject: Re: [gmx-users] Secondary structure after InflateGRO step - protein in lipid membrane On 10/11/12 5:57 AM, Shima Arasteh wrote: > I visualized the last output mdrun of KALP15-DPPC simulation, the secondary > structure of protein is complete and it seems OK. Can I trust on it and not > care about the visualization of system after inflategro? > > That's probably a reasonable conclusion. Sometimes visualization can be misleading. What you should trust the most is the outcome of the EM during shrinking of InflateGRO and whether it generates sensible forces. -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
