I am trying to do the NPT equilibration of a cyclic peptide in DMSO solvent BOX using all atom charm force field (ffcharmm27) on GROMACS. The NVT equilibration is working but the NPT equilibration shows the following ERROR.
Back Off! I just backed up results/eq50K.log to results/#eq50K.log.1# Reading file in1bar50K.tpr, VERSION 4.0.5 (double precision) Back Off! I just backed up results/eq50K.trr to results/#eq50K.trr.1# Back Off! I just backed up results/eq50K.xtc to results/#eq50K.xtc.1# Back Off! I just backed up results/eq50K.edr to results/#eq50K.edr.1# starting mdrun '16CHA in DMSO' 25000 steps, 50.0 ps. [2] Done nedit eq.csh Inner product between old and new vector <= 0.0! constraint #45 atoms 44 and 46 Wrote pdb files with previous and current coordinates Inner product between old and new vector <= 0.0! constraint #45 atoms 44 and 46 Wrote pdb files with previous and current coordinates Inner product between old and new vector <= 0.0! constraint #48 atoms 46 and 52 Wrote pdb files with previous and current coordinates Inner product between old and new vector <= 0.0! constraint #34 atoms 34 and 35 Wrote pdb files with previous and current coordinates Warning: 1-4 interaction between 26 and 36 at distance 153.333 which is larger than the 1-4 table size 2.400 nm These are ignored for the rest of the simulation This usually means your system is exploding, if not, you should increase table-extension in your mdp file or with user tables increase the table size Step 632 Warning: pressure scaling more than 1%, mu: 190.046 190.046 190.046 Inner product between old and new vector <= 0.0! constraint #39 atoms 38 and 39 Wrote pdb files with previous and current coordinates Step 633 Warning: pressure scaling more than 1%, mu: 252.207 252.207 252.207 Inner product between old and new vector <= 0.0! constraint #8 atoms 6 and 12 Wrote pdb files with previous and current coordinates Step 634 Warning: pressure scaling more than 1%, mu: 1.23498 1.23498 1.23498 Inner product between old and new vector <= 0.0! constraint #5 atoms 2 and 5 Wrote pdb files with previous and current coordinates There were 2 inconsistent shifts. Check your topology ------------------------------------------------------- Program mdrun, VERSION 4.0.5 Source code file: nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. ------------------------------------------------------- Corresponding .mdp file is as follows. ;*-------------START_[7.3]----------------------------------------------------------------------------------------- ;* ;*-------------GENERAL_[7.3.1]------------------------------------------------------------------------------------- ;* ;* User ;* ;* ;* ;* COMMENTS: ;* ;*-------------PREPROCESSING_[7.3.2]------------------------------------------------------------------------------- title = Free MD cpp = /lib/cpp ; Vorprozessor ;include ; Einfuegen von Topology-File-Verzeichnissen ;define = ; genaue Definition des Top-Files, z.B. Restraints ;* ;*-------------RUN_CONTROL_[7.3.3]--------------------------------------------------------------------------------- integrator = md ; Algorithmus: steep empfolen ;tinit dt = 0.002 ; [ZEIT: 0.001] Integrationsschritte in ps ! nsteps = 250000 ; [SCHRITTE: 0] Summe aller Integrationsschritte (aktuell: 10ps) ;init_step comm_mode = linear nstcomm = 500 ; [SCHRITTE: 1] Frequenz der Massenzentrumsbewegung comm_grps = system ;* ;*-------------LANGEVIN_DYNAMICS_[7.3.4]--------------------------------------------------------------------------- ;bd_temp ;bd_fric ld_seed = ;* ;*-------------ENERGY_MINIMIZATION_[7.3.5]------------------------------------------------------------------------- ;emtol = 100 ;emstep = 0.01 ;nstcgsteep = 50 ;nbfgscorr = 10 ;* ;*-------------SHELL_MOLECULAR_DYNAMICS_[7.3.6]-------------------------------------------------------------------- ;emtol ;niter ;* ;*-------------OUTPUT_CONTROL_[7.3.7]------------------------------------------------------------------------------ nstxout = 50000 ; [SCHRITTE: 100] Frequenz des Schreibens der Koordinaten nstvout = 50000 ; [SCHRITTE: 100] Frequenz des Schreibens der Geschwindigkeiten nstfout = 50000 ; [SCHRITTE: 0] Frequenz des Schreibens der Kraefte nstlog = 50000 ; [SCHRITTE: 100] Frequenz des Schreibens der Energien (in log-File) nstenergy = 500 ; [SCHRITTE: 100] Frequenz des Schreibens der Energien (in Energy-File) nstxtcout = 500 xtc_precision = 1000 xtc_grps = 16CHA energygrps = 16CHA DMSO ;* ;*-------------NEIGHBOUR_SEARCHING_[7.3.8]------------------------------------------------------------------------- nstlist = 5 ; [SCHRITTE: 10] Frequenz des Updates der Neighbour-List ns_type = grid ; Neighbour-Listen-Typ pbc = xyz rlist = 0.8 ;domain-decomposition = no ;* ;*-------------ELECTROSTATIC_&_VDW_[7.3.9]------------------------------------------------------------------------- coulombtype = reaction-field ;rcoulomb_switch = 0.0 rcoulomb = 1.4 ;epsilon_r = 1 epsilon_rf = 38 vdwtype = cut-off ;rvdw_switch = 0.0 rvdw = 1.4 ;dispcorr = ;table-extension ;fourierspacing = 0.12 ;(fourier_nx ;fourier_ny; fourier_nz) ;pme_order = 4 ;ewald_rtol = 1e-06 ;epsilon_surface = 0 ;ewald_geometry optimize_fft = yes ;* ;*--------------TEMPERATURE_COUPLING_[7.3.10]----------------------------------------------------------------------- tcoupl = v-rescale tc_grps = system tau_t = 0.1 ref_t = 50 ;* ;*--------------PRESSURE_COUPLING_[7.3.11]-------------------------------------------------------------------------- pcoupl = berendsen pcoupltype = isotropic tau_p = 2.0 compressibility = 5.22e-05 ; DMSO isothermal compressibility (for Water: 4.50e-05 bar-1) ref_p = 1.0 ;* ;*---------------SIMULATED_ANNEALING_[7.3.12]----------------------------------------------------------------------- ;annealing ;annealing_npoints ;annealing_time ;annealing_temp ;* ;*---------------VELOCITY_ GENERATION_[7.3.13]---------------------------------------------------------------------- gen_vel = no gen_temp = 50 gen_seed = 173529 ;* ;*---------------BONDS_[7.3.14]------------------------------------------------------------------------------------- constraints = all-bonds constraint_algorithm = shake continuation = yes shake_tol = 0.0001 ;lincs_order = 4 ;lincs_iter = 1 ;lincs_warnangle = 30 ;morse ;* ;*---------------ENERGY_GROUP_EXCLUSIONS_[7.3.15]------------------------------------------------------------------- ;energygrp_excl = ;* ;*---------------NMR_REFINEMENT_[7.3.16]---------------------------------------------------------------------------- ;disre ;disre_weighting ;disre_mixed ;disre_fc ;disre_tau ;nstdisreout ;orire ;orire_fc ;orire_tau ;orire_fitgrp ;nstorireout ;dihre ;dihre_fc ;dihre_tau ;nstdihreout ;* ;*---------------FREE_ENERGY_PERTURBATION_[7.3.17]------------------------------------------------------------------ ;free_energy = ;init_lambda = ;delta_lambda = ;sc_alpha = ;sc_power = ;sc_sigma = ;* ;*---------------NON-EQUILIBRIUM_MD_[7.3.18]------------------------------------------------------------------------ ;acc_grps ;accelerate ;freezegrps = ;freezedim = ;cos_acceleration ;* ;*---------------ELECTRIC_FIELDS_[7.3.19]--------------------------------------------------------------------------- ;(E_x; E_y; E_z) ;(E_xt; E_yt; E_zt) ;* ;*---------------USER_DEFINED_THINGIES_[7.3.20]--------------------------------------------------------------------- ;(user1_grps; user2_grps) ;(userint1; userint2; userint3; userint4) ;(userreal1; userreal2; userreal3; userreal4) ;* ;*---------------END_[7.3]------------------------------------------------------------------------------------------ I had a look on the archives list already and implemented the earlier suggested remarks but still the problem persists. Could you please suggest what could be the problem? Regards, Uday.
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