Hi, Did you try to debug your setup by running a normal single-replica simulation first?
Mark On Fri, Jan 5, 2018 at 12:12 PM Urszula Uciechowska < urszula.uciechow...@biotech.ug.edu.pl> wrote: > > > 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? 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