The energy minimization has been done and the result is as follow: Steepest Descents converged to Fmax < 100 in 8971 steps Potential Energy = -1.5253394e+06 Maximum force = 9.2729095e+01 on atom 4719 Norm of force = 3.5977371e+00
But by running mdrun, I get this fatal error: 1 particles communicated to PME node 4 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. So needs more npt? Thanks for your suggestions in advance. 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: Friday, April 19, 2013 10:02 PM Subject: Re: [gmx-users] unstable system On 4/19/13 1:18 PM, Shima Arasteh wrote: > Lets check the minim.mdp settings: > > ( ff applied is charmm36) > define = -DPOSRES > integrator = steep > emtol = 100.0 > emstep = 0.01 > nsteps = 50000 > nstlist = 1 > ns_type = grid > rlist = 1.2 > rlistlong = 1.4 > coulombtype = PME > rcoulomb = 1.2 > rvdw = 1.2 > vdwtype = switch > rvdw_switch = 1.0 > pbc = xyz > > > I would be grateful for your suggestions. > I see no reason to use restraints (doing so defeats the purpose of EM), but otherwise the settings are fine. -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
