Exactly. The reason I asked.... On Fri, Feb 20, 2015 at 1:14 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > > On 2/20/15 1:01 PM, HANNIBAL LECTER wrote: > >> Just out of curiosity what does -0.1 actually mean? >> >> > It means someone made a mistake :) It's not physically sensible. tau-t > should be a positive decimal or -1 to turn off coupling for that group. > Using -0.1 doesn't make any sense. It's probably the primary reason for > failure here. > > -Justin > > > On Fri, Feb 20, 2015 at 8:48 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 2/20/15 6:51 AM, Kalyanashis Jana wrote: >>> >>> Dear all, >>>> I am doing an MD simulation of a protein system. Energy minimization >>>> step >>>> has been completed smoothly but the position restraint MD run is not >>>> running properly(after 500-900 steps have been stopped automatically). >>>> Even >>>> it has not shown any error or anything. I have used a drug molecule in >>>> the >>>> cavity of the active site. >>>> When the box size was 10 X 12 X 25, it was run only 100 steps and with >>>> 15 >>>> X >>>> 15 X 28 box size it was run 500-900 steps. I could not understand what >>>> is >>>> the problem. Can anyone please help me? >>>> >>>> The pr.mdp file is >>>> cpp = /usr/bin/cpp >>>> define = -DPOSRES >>>> constraints = all-bonds >>>> integrator = md >>>> dt = 0.001 ; ps ! >>>> nsteps = 1000000 ; total 1000.0 ps. >>>> nstcomm = 100 >>>> nstxout = 250 ; ouput coordinates every 0.5 ps >>>> nstvout = 1000 ; output velocities every 2.0 ps >>>> nstfout = 0 >>>> nstlog = 100 >>>> nstenergy = 100 >>>> nstlist = 100 >>>> ns_type = grid >>>> rlist = 1.0 >>>> coulombtype = PME >>>> rcoulomb = 1.0 >>>> vdwtype = cut-off >>>> rvdw = 1.0 >>>> fourierspacing = 0.12 >>>> fourier_nx = 0 >>>> fourier_ny = 0 >>>> fourier_nz = 0 >>>> pme_order = 6 >>>> ewald_rtol = 1e-5 >>>> optimize_fft = yes >>>> ; V-rescale temparature coupling is on >>>> Tcoupl = V-rescale >>>> tau_t = 1.0 1.0 -0.1 1.0 1.0 >>>> tc_grps = SOL NA protein DRG CL >>>> ref_t = 300 300 300 300 300 >>>> >>>> >>> This thermostat setup is nonsensical. >>> >>> http://www.gromacs.org/Documentation/Terminology/ >>> Thermostats#What_Not_To_Do >>> >>> -Justin >>> >>> ; Pressure coupling is on >>> >>>> pcoupl = berendsen ; Use Parrinello-Rahman for research >>>> work >>>> pcoupltype = isotropic ; Use semiisotropic when working with >>>> membranes >>>> tau_p = 2.0 >>>> compressibility = 4.5e-5 >>>> ref_p = 1.0 >>>> refcoord-scaling = all >>>> ; Generate velocites is on at 300 K. >>>> gen_vel = yes >>>> gen_temp = 300.0 >>>> gen_seed = 173529 >>>> >>>> >>>> Thanks in advance, >>>> Kalyanashis Jana. >>>> >>>> >>>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/ >>> Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >>> send a mail to gmx-users-requ...@gromacs.org. >>> >>> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.