Thanks Justin. One component I mean system of only one type atom, each atom has two charged virtual sites. So I can not see from VMD any breaking.
On Dec 17, 2017 8:10 PM, "Justin Lemkul" <jalem...@vt.edu> wrote: On 12/17/17 8:22 AM, Faezeh Pousaneh wrote: > Dear Justin, > > How can I check that ''input configuration is "broken" across PBC'' ? > From vmd it is hard to say, since I only have one component system. > What is that one component? If a group of atoms is supposed to be in a charge group, and it is split across the box, then you need to correct it with trjconv or (if you are absolutely sure this isn't a problem) override with grompp -maxwarn (dangerous and generally not wise). -Justin > Best regards > > > On Fri, Dec 15, 2017 at 2:05 PM, Faezeh Pousaneh <fpoosa...@gmail.com> > wrote: > > The sum of the two largest charge group radii (7.984601) is larger than >> rlist (0.347900). >> the configuration looks fine across pbc. Everything looks normal. >> Following is my md. I have user-specified potential so I need to have >> cut-off values as given below. >> >> >> integrator = md >> dt = 0.001 >> nsteps = 3000000 >> nstxout = 100000 ; save coordinates every 0 >> ps >> nstvout = 100000 ; save velocities every 0 >> ps >> nstlog = 100000 ; update log file every >> nstenergy = 100000 ; save energies every >> nstxtcout = 100000 ; Output frequency for xtc file >> xtc-precision = 100000 ; precision for xtc file >> ns_type = grid ; search neighboring grid cells >> nstlist = 10 ; fs >> pbc = xyz ; 3-D PBC >> rlist = 0.3479 ; short-range neighborlist >> cutoff >> (in nm) >> rcoulomb = 0.3479 ; short-range electrostatic >> cutoff (in nm) >> rvdw = 0.3479; short-range van der Waals cutoff (in nm) >> coulombtype = PME-user ; Particle Mesh Ewald for >> long-range electrostatics >> pme_order = 4 ; cubic interpolation >> fourierspacing = 0.16 ; grid spacing for FFT >> vdw-type = user >> Tcoupl = berendsen ; modified Berendsen thermostat >> tc-grps = co2 rest ; two coupling groups - >> more accurate >> tau_t = 0.1 0.1 ; time constant, in ps >> ref_t = 179.8 179.8 ; reference temperature, one >> for each group, in K >> ;tc-grps = system >> cutoff-scheme =group >> energygrps = co2 rest >> Pcoupl = no;Parrinello-Rahman >> Pcoupltype = Isotropic >> tau_p = 1.0 >> compressibility = 6.2e-5 >> ref_p = 50.0 >> gen_vel = yes >> gen_temp = 179.8 >> gen_seed = 712349 >> DispCorr =no; EnerPres ; account for cut-off vdW >> scheme >> constraints = all-bonds ; all bonds constrained (fixed >> length) >> continuation = no ; Restarting after NPT >> constraint-algorithm = lincs ; holonomic constraints >> lincs_iter = 1 ; accuracy of LINCS >> lincs_order = 4 ; also related to accuracy >> >> >> >> Best regards >> >> >> On Fri, Dec 15, 2017 at 1:44 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> On 12/15/17 4:26 AM, Faezeh Pousaneh wrote: >>> >>> Hi, >>>> >>>> I get this error only in NVT equlibration step, not in the NPT and >>>> production steps. Should I worry about it? >>>> >>>> In gromacs page it tell the error can come from 4 reasons, but how I can >>>> recognize which can be mine? >>>> >>>> Check the size of your largest charge group, value of rlist, or whether >>> or not the input configuration is "broken" across PBC. >>> >>> -Justin >>> >>> http://www.gromacs.org/Documentation/Errors?highlight=docume >>> >>>> ntation#The_sum_of_the_two_largest_charge_group_radii_(X) >>>> _is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb >>>> >>>> Best regards >>>> >>>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Assistant Professor >>> Virginia Tech Department of Biochemistry >>> >>> 303 Engel Hall >>> 340 West Campus Dr. >>> Blacksburg, VA 24061 >>> >>> jalem...@vt.edu | (540) 231-3129 >>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html >>> >>> ================================================== >>> >>> -- >>> 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. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- 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.