Hey Gyorgy, Your current topology file(s) is(are) also important to analyze the situation and fix the problem.
Pass my kind regards to Julia... ======================== Dr. Vitaly V. Chaban, Ph.D. Department of Chemistry University of Rochester Rochester, New York 14627-0216 The United States of America ========================= > The mdp file is attached. > Best, > Gyorgy > > Quoting "Justin A. Lemkul" <jalem...@vt.edu>: > >> >> >> gyorgy.han...@fc.up.pt wrote: >>> >>> Dear all, >>> >>> I am setting up a simulation of ionic liquids with the PF6 anion. >>> According to the potential, the anion should be kept rigid, wich >>> obviously means that bond lengths and angles have to be >>> constrained. LINCS doesn't work with angle constraints (i.e. >>> constraing a triangle), so we decided to use SHAKE. However, SHAKE >>> seems to work a bit strangely: I know SHAKE mustn't be used with >>> domain decomposition, but even if I set the corresponding variable >>> to NO in the mdp file, the simulation crashes on 8 procs and gives >>> the following error message: >>> >>> Fatal error: >>> 1 particles communicated to PME node 7 are more than a cell length >>> out of the domain decomposition cell of their charge group. >>> >>> If I try to run mdrun with -pd (to 'really' switch off domain >>> decomposition), the simulation doesn't chrash but gives nonsense >>> (the energy seems to increase constantly). >>> >>> I am not an expert user so maybe I do something wrong but, anyway, >>> does anyone have an idea how to constrain this anion with Gromacs? >>> I checked mailing list archive but couldn't find any answer >>> corresponding to my question. >>> >> >> Without seeing a complete .mdp file, it's not possible to fully >> diagnose this problem. The combination of SHAKE + particle >> decomposition should be stable, but there are a whole host of different >> things that can go wrong. >> >> -Justin >> >>> Thanks in advance. >>> >>> Gyorgy >>> >>> >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -------------- next part -------------- > title = BMIM PF6 bulk simulation > cpp = /usr/bin/cpp > > ; RUN CONTROL PARAMETERS ;l_bfgs > integrator = md;steep > ; Start time and timestep in ps > tinit = 0 > dt = 0.00000001 ! just to see if it starts > nsteps = 25000 > ; mode for center of mass motion removal > comm-mode = linear > ; number of steps for center of mass motion removal > nstcomm = 10 > ; group(s) for center of mass motion removal > > ; ENERGY MINIMIZATION OPTIONS > ; Force tolerance and initial step-size > ;emtol = 50 > ;emstep = 0.5 > ;lincs_iter = 3 > ;lincs_warnangle = 50 > ; Frequency of steepest descents steps when doing CG > ;nstcgsteep = 1000 > ;nbfgscorr = 10 > > ; OUTPUT CONTROL OPTIONS > ; Output frequency for coords (x), velocities (v) and forces (f) > nstxout = 0 > nstvout = 0 > nstfout = 0 > ; Checkpointing helps you continue after crashes > nstcheckpoint = 10000 > ; Output frequency for energies to log file and energy file > nstlog = 10000 > nstenergy = 10000 > ; Output frequency and precision for xtc file > nstxtcout = 10000 > xtc-precision = 1000 > ; This selects the subset of atoms for the xtc file. You can > ; select multiple groups. By default all atoms will be written. > xtc-grps = > ; Selection of energy groups > energygrps = > > ; NEIGHBORSEARCHING PARAMETERS > ; nblist update frequency > nstlist = 25 > ; ns algorithm (simple or grid) > ns_type = grid > ; Periodic boundary conditions: xyz (default), no (vacuum) > ; or full (infinite systems only) > pbc = xyz > ; nblist cut-off > rlist = 1.5 > domain-decomposition = no > > ; OPTIONS FOR ELECTROSTATICS AND VDW > ; Method for doing electrostatics > coulombtype = PME ; can RF also be used? > rcoulomb-switch = 0 > rcoulomb = 1.5 > ; Dielectric constant (DC) for cut-off or DC of reaction field > epsilon_rf = > ; Method for doing Van der Waals > vdw-type = Shift > ; cut-off lengths > rvdw-switch = 1.1 > rvdw = 1.2 > ; Apply long range dispersion corrections for Energy and Pressure > DispCorr = EnerPres > ; Extension of the potential lookup tables beyond the cut-off > table-extension = 1 > ; Spacing for the PME/PPPM FFT grid > fourierspacing = 0.12 > ; FFT grid size, when a value is 0 fourierspacing will be used > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters > pme_order = 4 > ewald_rtol = 1e-05 > ewald_geometry = 3d > epsilon_surface = 0 > optimize_fft = no > > ; OPTIONS FOR WEAK COUPLING ALGORITHMS > ; Temperature coupling > Tcoupl = V-rescale > ; Groups to couple separately > tc-grps = System > ; Time constant (ps) and reference temperature (K) > tau_t = 1.0 > ref_t = 298.15 > ; Pressure coupling > Pcoupl = Parrinello-Rahman > Pcoupltype = isotropic > ; Time constant (ps), compressibility (1/bar) and reference P (bar) > tau_p = 4.0 > compressibility = 4.5e-5 ; proper value for IL??? > ref_p = 1.00 > > ; SIMULATED ANNEALING > ; Type of annealing for each temperature group (no/single/periodic) > ; annealing = no > > ; GENERATE VELOCITIES FOR STARTUP RUN > gen_vel = yes > gen_temp = 298.15 > gen_seed = 1993 > > ; OPTIONS FOR BONDS > constraints = hbonds > constraint_algorithm = SHAKE -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! 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