Hi, I should run it by using mdrun_mpi?
best Urszula > Hello, > > From my experience, the domain decomposition is not compatible with > implicit solvent, you have to switch > to particle decomposition for the simulations. > > > All the best, > Qinghua > > On 01/05/2018 12:40 PM, Urszula Uciechowska wrote: >> 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. -------------------------------------------- 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.