@Justin, Fmax=8.0226669e+00 the system includes protein, lipid, water, ion Cl-
em.mdp file is integrator = steep tinit = 0.0 dt = 0.02 nsteps = 50000 nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 xtc_precision = 1000 nstlist = 1 ns_type = grid pbc = xyz rlist = 1.4 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r = 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = no pcoupl = no gen_vel = no constraints = none constraint_algorithm = Lincs continuation = no lincs_order = 4 lincs_warnangle = 30 equi.mdp file is integrator = md tinit = 0.0 dt = 0.03 nsteps = 3000000 nstcomm = 1 comm-grps = nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 1000 nstenergy = 1000 nstxtcout = 1000 xtc_precision = 100 xtc-grps = energygrps = nstlist = 10 ns_type = grid pbc = xyz rlist = 1.2 coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 epsilon_r = 15 vdw_type = Shift rvdw_switch = 0.9 rvdw = 1.2 DispCorr = No tcoupl = Berendsen tc-grps = Protein DSPC Ion_W tau_t = 1.5 1.5 1.5 ref_t = 310 310 310 Pcoupl = Berendsen Pcoupltype = semiisotropic tau_p = 3.0 3.0 compressibility = 3e-4 3e-4 ref_p = 1.0 1.0 gen_vel = no constraints = none constraint_algorithm = Lincs continuation = no lincs_order = 4 lincs_warnangle = 30 Thanks so much for any help ! Regards, KT On Sun, Jan 27, 2013 at 8:26 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote: > >> Thank Tsjerk so much ! >> But after being minimized 50000 steps and equilibrated 90 ns, there are >> some bonds in the system that rotate more than 30 degrees. >> I applied tips for blew up system as you advised. But the system does not >> achieve balance. >> Should i carry out more many steps for minimization ? or minimize many >> times ? to get more equilibrated system. >> >> > I would say that 50000 steps of minimization is far more than is normally > necessary. What Fmax do you achieve at the end of EM? What is in the > system? What is in your .mdp file? Systems can randomly crash if the model > physics breaks due to incorrect .mdp settings or an unstable topology. > > -Justin > > > On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar <tsje...@gmail.com >> >wrote: >> >> Hi KT, >>> >>> This is caused by another problem. Your system blew up. Check messages >>> before this one, and check the log for LINCS warnings. >>> >>> Cheers, >>> >>> Tsjerk >>> >>> On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen <kieuthu2...@gmail.com >>> >>>> wrote: >>>> >>> >>> Dear All, >>>> >>>> My MD simulation has an error >>>> >>>> Warning: Only triclinic boxes with the first vector parallel to the >>>> >>> x-axis >>> >>>> and the second vector in the xy-plane are supported. >>>> Box (3x3): >>>> Box[ 0]={ nan, nan, nan} >>>> Box[ 1]={ nan, nan, nan} >>>> Box[ 2]={ nan, nan, nan} >>>> Can not fix pbc. >>>> >>>> I searched on Gromacs-errors web, but i did not see this error. >>>> How can i fix it ? >>>> >>>> Thanks and regards, >>>> KT >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> * Please search the archive at >>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >>>> >>>> >>> >>> >>> -- >>> Tsjerk A. Wassenaar, Ph.D. >>> >>> post-doctoral researcher >>> Biocomputing Group >>> Department of Biological Sciences >>> 2500 University Drive NW >>> Calgary, AB T2N 1N4 >>> Canada >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >>> >>> > -- > ==============================**========== > > 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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? 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