Dear gromacs users,
I am trying to run REMD simulations using 4.5.5 version (implicit solvent). The MD procedure: pdb2gmx -f prot.pdb -o prot.gro -q prot.pdb -ignh -ss. The input for minimization step: ; Run control parameters integrator = cg nsteps = 8000000 vdwtype = cut-off coulombtype = cut-off ;cutoff-scheme = group pbc = no periodic_molecules = no nstlist = 10 ns_type = grid rlist = 1.0 rcoulomb = 1.6 rvdw = 1.6 comm-mode = Angular nstcomm = 10 ; ;Energy minimizing stuff ; emtol = 100.0 nstcgsteep = 2 emstep = 0.01 ; ;Relative dielectric constant for the medium and the reaction field epsilon_r = 1 epsilon_rf = 1 ; ; Implicit solvent ; implicit_solvent = GBSA gb_algorithm = OBC ;Still HCT OBC nstgbradii = 1.0 rgbradii = 1.0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA. The value -1 will set default value for Still/HCT/OBC GB-models. and it finished without errors. The problem is with equilibration step. The input file that I used is: ; MD CONTROL OPTIONS integrator = md dt = 0.002 nsteps = 50000 ; 10 ns init_step = 0 ; For exact run continuation or redoing part of a run comm-mode = Angular ; mode for center of mass motion removal nstcomm = 10 ; number of steps for center of mass motion removal ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 1000 nstvout = 1000 nstfout = 1000 ; Output frequency for energies to log file and energy file nstlog = 1000 nstcalcenergy = 10 nstenergy = 1000 ; Neighbor searching and Electrostatitcs vdwtype = cut-off coulombtype = cut-off ;cutoff-scheme = group pbc = no periodic_molecules = no nstlist = 5 ns_type = grid rlist = 1.0 rcoulomb = 1.6 rvdw = 1.0 ; Selection of energy groups energygrps = fixed not_fixed freezegrps = fixed not_fixed freezedim = Y Y Y N N N ;Relative dielectric constant for the medium and the reaction field epsilon_r = 1 epsilon_rf = 1 ; Temperutare coupling tcoupl = v-rescale tc_grps = fixed not_fixed tau_t = 0.01 0.01 ;nst_couple = 5 ref_t = 300.00 300.00 ; Pressure coupling pcoupl = no ;pcoupletype = isotropic tau_p = 1.0 ;compressiblity = 4.5e-5 ref_p = 1.0 gen_vel = yes gen_temp = 300.00 300.00 gen_seed = -1 constraints = h-bonds ; Implicit solvent implicit_solvent = GBSA gb_algorithm = Still ; HCT ; OBC nstgbradii = 1.0 rgbradii = 1.0 ; [nm] Cut-off for the calculation of the Born radii. Currently must be equal to rlist gb_epsilon_solvent = 80 ; Dielectric constant for the implicit solvent gb_saltconc = 0 ; Salt concentration for implicit solvent models, currently not used sa_algorithm = Ace-approximation sa_surface_tension = 2.05016 ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA. The value -1 will set default value for Still/HCT/OBC GB-models. mdrun -v -multidir eq_[12345678] The error that I obtained is: Fatal error: A charge group moved too far between two domain decomposition steps This usually means that your system is not well equilibrated For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I do not know what is wrong. I checked the Fatal error at www.gromacs.org/Documentation/Errors. My system is ok, I tried to increase the min steps but did not help. I have also checked the http://www.gromacs.org/Documentation/How-tos/REMD but can not move forward because of equilibration step. I appreciate any recommendation. Thanks Urszula -------------------------------------------- Urszula Uciechowska PhD University of Gdansk and Medical Univesity of Gdansk Department of Molecular and Cellular Biology ul. Abrahama 58 80-307 Gdańsk Poland ----------------------------------------- Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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.