Hi, I just run a normal single-replica. Now the error that I have is:
Program mdrun_mpi, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Any suggestions? What can I do to run it? Thanks Ula > 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? 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. -------------------------------------------- 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.