On Wed, Apr 10, 2013 at 3:49 PM, Liron Cohen <liron.co...@weizmann.ac.il>wrote:
> hi, > > i am using gromacs 4.5 and i am trying to run an energy minimization and > then temperature equilibration for a system of two charged plates plates > solvented in water. > the plates are made of fake atoms which has carbon atoms parameters, and a > bond length of 0.2 nm. > > the plates are made from o configuration of 6x6 of these atoms. each > located in a distance of 0.2 nm from the other. > > energy minimization is working just fine, but as i try to run the > temperature equilibration i get the following warning: > > Warning: 1-4 interaction between 49 and 67 at distance 6.967 which is > larger than the 1-4 table size 2.000 nm > These are ignored for the rest of the simulation > > and also a bunch of these warnings: > t = 0.019 ps: Water molecule starting at atom 8260 can not be settled. > > > the EM file is: > > title = Test_mg_water > cpp = /usr/bin/cpp -traditional; the c pre-processor > define = -DFLEXIBLE > constraints = none > integrator = steep > dt = 0.002 ; ps ! > nsteps = 100000 > nstxout = 100 > nstlist = 1 > ns_type = grid > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > rvdw = 1.4 > fourierspacing = 0.12 > optimize_fft = yes > pme_order = 4 > ewald_rtol = 1e-5 > ; > ; Energy minimizing stuff > ; > emtol = 100.0 > emstep = 0.01 > ; freeze the solute and ions > > freezegrps = GAP GAN > freezedim = Y Y Y Y Y Y > energygrps = GAP GAN > > > *************************** (GAP and GAN are the charged plates) > > the temperature equilibration file is: > title = Heat@constant volume > cpp = /usr/bin/cpp -traditional; the c pre-processor > ; > define = -DPOSRES > ; > constraints = none > nstlist = 1 > pbc = xyz > rlist = 1.0 > ;domain-decomposition = yes > coulombtype = PME-switch > rcoulomb = 0.9 > > epsilon-r = 1 > vdw-type = switch > rvdw-switch = 0.8 > rvdw = 0.9 > DispCorr = EnerPres > epsilon_surface = 0 > integrator = sd > tinit = 0 > dt = 0.002 > nsteps = 37500 ; 75 psec > nstcomm = 1000 > nstfout = 0 > ;kys > nstlog = 1000 > nstenergy = 100 > nstxtcout = 100 > nstxout = 100 > nstvout = 50000 > xtc_precision = 1000 > xtc_grps = SYSTEM > ns_type = grid > tc_grps = SYSTEM > tau_t = 0.1 > ref_t = 300 > ;tcoupl = nose-hoover > ;constraints = hbonds > constraint-algorithm = Lincs > ;unconstrained-start = no > shake-tol = 0.0001 > lincs-order = 4 > lincs-warnangle = 30 > lincs_iter = 2 > ;freezegrps = SFP SFN > ;freezedim = Y Y Y Y Y Y > > fourierspacing = 0.12 > > pme_order = 4 > ewald_rtol = 1e-5 > optimize_fft = yes > > ; Type of annealing for each temperature group (no/single/periodic) > annealing = single > ; Number of time points to use for specifying annealing in each group > annealing_npoints = 4 > ; List of times at the annealing points for each group > annealing_time = 0 25 50 75 > ; Temp. at each annealing point, for each group. > annealing_temp = 5 150 300 300 > > gen_seed = 6594 > gen_temp = 5 > > > the initial coordinates of the plates are: > > Good ROcking Metal Altar for Chronical Sinners > 72 > 1GAP G1 1 1.750 2.000 1.750 > 1GAP G2 2 1.750 2.000 1.950 > 1GAP G3 3 1.750 2.000 2.150 > 1GAP G4 4 1.750 2.000 2.350 > 1GAP G5 5 1.750 2.000 2.550 > 1GAP G6 6 1.750 2.000 2.750 > 1GAP G7 7 1.950 2.000 1.750 > 1GAP G8 8 1.950 2.000 1.950 > 1GAP G9 9 1.950 2.000 2.150 > 1GAP G10 10 1.950 2.000 2.350 > 1GAP G11 11 1.950 2.000 2.550 > 1GAP G12 12 1.950 2.000 2.750 > 1GAP G13 13 2.150 2.000 1.750 > 1GAP G14 14 2.150 2.000 1.950 > 1GAP G15 15 2.150 2.000 2.150 > 1GAP G16 16 2.150 2.000 2.350 > 1GAP G17 17 2.150 2.000 2.550 > 1GAP G18 18 2.150 2.000 2.750 > 1GAP G19 19 2.350 2.000 1.750 > 1GAP G20 20 2.350 2.000 1.950 > 1GAP G21 21 2.350 2.000 2.150 > 1GAP G22 22 2.350 2.000 2.350 > 1GAP G23 23 2.350 2.000 2.550 > 1GAP G24 24 2.350 2.000 2.750 > 1GAP G25 25 2.550 2.000 1.750 > 1GAP G26 26 2.550 2.000 1.950 > 1GAP G27 27 2.550 2.000 2.150 > 1GAP G28 28 2.550 2.000 2.350 > 1GAP G29 29 2.550 2.000 2.550 > 1GAP G30 30 2.550 2.000 2.750 > 1GAP G31 31 2.750 2.000 1.750 > 1GAP G32 32 2.750 2.000 1.950 > 1GAP G33 33 2.750 2.000 2.150 > 1GAP G34 34 2.750 2.000 2.350 > 1GAP G35 35 2.750 2.000 2.550 > 1GAP G36 36 2.750 2.000 2.750 > 2GAN G1 37 1.750 5.000 1.750 > 2GAN G2 38 1.750 5.000 1.950 > 2GAN G3 39 1.750 5.000 2.150 > 2GAN G4 40 1.750 5.000 2.350 > 2GAN G5 41 1.750 5.000 2.550 > 2GAN G6 42 1.750 5.000 2.750 > 2GAN G7 43 1.950 5.000 1.750 > 2GAN G8 44 1.950 5.000 1.950 > 2GAN G9 45 1.950 5.000 2.150 > 2GAN G10 46 1.950 5.000 2.350 > 2GAN G11 47 1.950 5.000 2.550 > 2GAN G12 48 1.950 5.000 2.750 > 2GAN G13 49 2.150 5.000 1.750 > 2GAN G14 50 2.150 5.000 1.950 > 2GAN G15 51 2.150 5.000 2.150 > 2GAN G16 52 2.150 5.000 2.350 > 2GAN G17 53 2.150 5.000 2.550 > 2GAN G18 54 2.150 5.000 2.750 > 2GAN G19 55 2.350 5.000 1.750 > 2GAN G20 56 2.350 5.000 1.950 > 2GAN G21 57 2.350 5.000 2.150 > 2GAN G22 58 2.350 5.000 2.350 > 2GAN G23 59 2.350 5.000 2.550 > 2GAN G24 60 2.350 5.000 2.750 > 2GAN G25 61 2.550 5.000 1.750 > 2GAN G26 62 2.550 5.000 1.950 > 2GAN G27 63 2.550 5.000 2.150 > 2GAN G28 64 2.550 5.000 2.350 > 2GAN G29 65 2.550 5.000 2.550 > 2GAN G30 66 2.550 5.000 2.750 > 2GAN G31 67 2.750 5.000 1.750 > 2GAN G32 68 2.750 5.000 1.950 > 2GAN G33 69 2.750 5.000 2.150 > 2GAN G34 70 2.750 5.000 2.350 > 2GAN G35 71 2.750 5.000 2.550 > 2GAN G36 72 2.750 5.000 2.750 > 4.50000 7.00000 4.50000 > > the 4.5 7 4.5 are the dimentions of the box/ > > i want to know what do i do wrong and why do i keep getting this warning : > > Warning: 1-4 interaction between 49 and 67 at distance 6.967 which is > larger than the 1-4 table size 2.000 nm > These are ignored for the rest of the simulation > Your system is blowing up because it's unstable. Where did you get this protocol? I suggest starting by reproducing something similar that has been published :-) Mark -- 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
