Hi Qasim, > On 11 Jan 2017, at 20:29, Qasim Pars <qasimp...@gmail.com> wrote: > > Dear Carsten, > > Thanks. The forward state simulations works properly with mdrun -ntmpi 8 > -ntomp 2 or mdrun -ntmpi 4 -ntomp 4 as you suggested. > For the backward state GROMACS still gives too many lincs warning error > with those mdrun commands in the md step, indicating the system is far from > equilibrium. I used the below free energy parameters with the em, nvt, npt > and md steps for the backward state (fast growth). And to keep the ligand > in the active site of protein I use some restraints under the > intermolecular_interactions in the top file as I told in my previous email. > > free-energy = yes > init-lambda = 1 > delta-lambda = 0 > sc-alpha = 0.3 > sc-power = 1 > sc-sigma = 0.25 > sc-coul = yes > couple-moltype = ligand > couple-intramol = no > couple-lambda0 = vdw-q > couple-lambda1 = none > nstdhdl = 100 > > My questions: > > 1) Do you think that I should use the above free energy paramaters in all > MD steps (em, nvt, npt and md)? I think you want them only in the MD part.
> > 2) The structure seems fine before arising the lincs warning. First linc > warning belongs to protein atoms (not ligand atoms). However the ligand > doesn't move out of the active site. Maybe the following mdp file for the > md step is not correct or the backward state simulation of a complex > structure is something impossible with GROMACS? It should work in both directions. Why is your delta-lambda zero in your snippets? > > 3) Maybe the intermolecular_interactions section and couple- flags don't > turn off intramolecular interactions of the ligand and turn on state B? > > 4) How can I get rid of the linc warnings in the md step? How many LINCS warnings do you get? Does you system blow up? Carsten > > #md.mdp: > > ; RUN CONTROL > integrator = sd > nsteps = 50000000 > dt = 0.002 > comm-mode = Linear > nstcomm = 100 > > ; OUTPUT CONTROL > nstxout-compressed = 500 > compressed-x-precision = 1000 > nstlog = 500 > nstenergy = 500 > nstcalcenergy = 100 > > ; BONDS > constraint_algorithm = lincs > constraints = all-bonds > lincs_iter = 1 > lincs_order = 4 > lincs-warnangle = 30 > continuation = no > > ; NEIGHBOUR SEARCHING > cutoff-scheme = verlet > ns-type = grid > nstlist = 20 > pbc = xyz > > ; ELECTROSTATICS-EWALD > coulombtype = PME > rcoulomb = 1.0 > ewald_geometry = 3d > pme-order = 4 > fourierspacing = 0.12 > > ; VAN DER WAALS > vdwtype = Cut-off > rvdw = 1.0 > rvdw-switch = 0.9 > DispCorr = EnerPres > > ; TEMPERATURE COUPLING (SD - Langevin dynamics) > tc_grps = Protein ligand > tau_t = 1.0 1.0 > ref_t = 298.15 298.15 > > ; PRESSURE COUPLING > pcoupl = Parrinello-Rahman > pcoupltype = isotropic > tau_p = 2 > ref_p = 1.0 > compressibility = 4.5e-05 > > ; VELOCITY GENERATION > gen_vel = yes > gen_seed = -1 > gen_temp = 298.15 > > ;FREE ENERGY > free-energy = yes > init-lambda = 1 > delta-lambda = 0 > sc-alpha = 0.3 > sc-power = 1 > sc-sigma = 0.25 > sc-coul = yes > couple-moltype = ligand > couple-intramol = no > couple-lambda0 = vdw-q > couple-lambda1 = none > nstdhdl = 100 > > Thanks in advance. > > On 11 January 2017 at 10:49, Kutzner, Carsten <ckut...@gwdg.de> wrote: > >> Dear Qasim, >> >> those kinds of domain decomposition 'errors' can happen when you >> try to distibute an MD system among too many MPI ranks. There is >> a minimum cell length for each domain decomposition cell in each >> dimension, which depends on the chosen cutoff radii and possibly >> other inter-atomic constraints. So this is normally just a technical >> limitation and not a problem with the MD system. >> >> You can do the following steps to circumvent that issue: >> >> a) use less ranks (at the domain decomposition limit, the parallel >> efficiency suffers anyway) >> >> b) use separate PME ranks, so that you get less and larger domains >> on the MPI ranks that do domain decomposition >> (use mdrun -nt 20 -npme 4 ... for example, you will have to try >> around a bit with the exact number of PME ranks for optimal >> performance - or use the gmx tune_pme tool for that!) >> >> c) In case you haven't done so already, compile GROMACS with >> MPI *and* OpenMP. Then, by using MPI domain decomposition plus >> OpenMP parallelism within each MPI rank, you will be >> able to use more cores in parallel even for smaller MD systems. >> >> Use mdrun -ntmpi 10 -ntomp 2 for 10 ranks * 2 threads or >> mdrun -ntmpi 4 -ntomp 5 for 4 ranks * 5 threads >> >> With real MPI, you would use something like >> >> mpirun -np 10 gmx mdrun -ntomp 2 ... >> >> Don't forget to check your simulation performance, there will >> be better and worse choices in terms of these decomposition parameters. >> >> Happy simulating! >> Carsten >> >> >>> On 11 Jan 2017, at 08:33, Qasim Pars <qasimp...@gmail.com> wrote: >>> >>> Dear users, >>> >>> I am trying to simulate a protein-ligand system including ~20000 atoms >> with >>> waters using GROMACS-2016.1. The protocol I tried is forward state for >> the >>> free energy calculation. The best ligand pose used in the simulations was >>> got by AutoDock. At the beginning of the simulation GROMACS suffers from >>> domain decomposition error in the energy minimization step: >>> >>> Fatal error: >>> There is no domain decomposition for 20 ranks that is compatible with the >>> given box and a minimum cell size of 1.7353 nm >>> Change the number of ranks or mdrun option -rdd >>> Look in the log file for details on the domain decomposition >>> >>> I checked the complex structure visually. I don't see any distortion in >> the >>> structure. To check whether the problem is the number of nodes, I used 16 >>> nodes: >>> >>> gmx mdrun -v -deffnm em -nt 16 >>> >>> The energy minimization step was completed successfully. For the NVT >> step I >>> used 16 nodes again. >>> >>> gmx mdrun -v -deffnm nvt -nt 16 >>> >>> After ~2000000 steps the system gave too many lincs warning. >>> >>> Whereas there is no problem with wild type protein when it is simulated >>> without using -nt 16. These domain decomposition error and lincs warning >>> arise for complex structure. >>> >>> By the way to keep the ligand in the active site of protein I use the >> bond, >>> angle and dihedral restraints under [ intermolecular_interactions ] >> section >>> in the top file. >>> >>> [ intermolecular_interactions ] >>> [ bonds ] >>> 313 17 10 0.294 0.294 10.000 0.000 0.294 >>> 0.294 10.000 4184.000 >>> >>> [ angle_restraints ] >>> 312 313 17 313 1 140.445 0.000 1 >>> 140.445 41.840 1 >>> 313 17 19 17 1 107.175 0.000 1 >>> 107.175 41.840 1 >>> >>> [ dihedral_restraints ] >>> 300 312 313 17 1 56.245 0.000 0.000 >>> 56.245 0.000 41.840 >>> 312 313 17 19 1 -3.417 0.000 0.000 >>> -3.417 0.000 41.840 >>> 313 17 19 14 1 -110.822 0.000 0.000 >>> -110.822 0.000 41.840 >>> >>> The mdp file used for the energy minimization is follows: >>> >>> define = -DFLEXIBLE >>> integrator = steep >>> nsteps = 50000 >>> emtol = 1000.0 >>> emstep = 0.01 >>> nstcomm = 100 >>> >>> ; OUTPUT CONTROL >>> nstxout-compressed = 500 >>> compressed-x-precision = 1000 >>> nstlog = 500 >>> nstenergy = 500 >>> nstcalcenergy = 100 >>> >>> ; BONDS >>> constraints = none >>> >>> ; NEIGHBOUR SEARCHING >>> >>> cutoff-scheme = verlet >>> ns-type = grid >>> nstlist = 10 >>> pbc = xyz >>> >>> ; ELECTROSTATICS & EWALD >>> coulombtype = PME >>> rcoulomb = 1.0 >>> ewald_geometry = 3d >>> pme-order = 4 >>> fourierspacing = 0.12 >>> >>> ; VAN DER WAALS >>> vdwtype = Cut-off >>> vdw_modifier = Potential-switch >>> rvdw = 1.0 >>> rvdw-switch = 0.9 >>> DispCorr = EnerPres >>> >>> ; FREE ENERGY >>> free-energy = yes >>> init-lambda = 0 >>> delta-lambda = 0 >>> sc-alpha = 0.3 >>> sc-power = 1 >>> sc-sigma = 0.25 >>> sc-coul = yes >>> couple-moltype = ligand >>> couple-intramol = no >>> couple-lambda0 = vdw-q >>> couple-lambda1 = none >>> nstdhdl = 100 >>> >>> I removed the free energy lines in the em.mdp and [ >>> intermolecular_interactions ] section in the top file but GROMACS still >>> gives the domain decomposition error for the complex structure. >>> >>> Will you please give suggestions on getting rid of the lincs warning and >>> domain decomposition messages? >>> >>> I would appreciate any kind of help. >>> >>> Thanks. >>> >>> -- >>> Qasim Pars >>> -- >>> 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. >> > > > > -- > Qasim Pars > -- > 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.