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.
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. >> > > -- 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.
