On Tue, Dec 20, 2011 at 7:16 PM, Mark Abraham <[email protected]> wrote: > On 12/19/2011 1:51 PM, Ben Reynwar wrote: >> >> I'm having a problem with gromacs not terminating as expected when >> using the maxh option. >> It is an REMD simulation with 32 replicas. >> I'm specifying -maxh 24 and as expected see the following in the stderr >> output. >> >> Step 773882: Run time exceeded 23.760 hours, will terminate the run >> >> Step 773876: Run time exceeded 23.760 hours, will terminate the run >> >> Step 773880: Run time exceeded 23.760 hours, will terminate the run >> >> etc >> >> However I can see that the output files continued to be written for >> another hour until at 25 hours the simulation was terminated by the >> queueing system. >> No checkpoint files were produced. The output files show that the >> simulation continued until about step 797000. >> >> I've done similar things previously without running into this problem. >> Anyone have any ideas for what stupid mistake I could be making? > > > Perhaps none. What GROMACS version is this? Does the latest version have the > same behaviour? > > Mark > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Sorry for the slow response. I've been away on holiday. The version used is 4.5.5 with a bug fix applied from http://lists.gromacs.org/pipermail/gmx-developers/2011-October/005405.html It was a replica exchange simulation. I've narrowed down the problem to be specific to using infinite cutoff. With a finite cutoff there are no problems. The initial run works fine and creates checkpoints. However a run started from one of these checkpoints fails to create checkpoints itself. The diff between the an mdp that works fine and one that doesn't is: 53,57c53,58 < ; [nm] cut-off distance for the short-range neighbor list. < ; Set to zero for infinite cut-off. < rlist = 0 < ; Recalculating pair-list is not necessary with an infinite cut-off < nstlist = 0 --- > ; [nm] cut-off distance for the short-range neighbor list > ; For Generalized Born this must be equal to the cut-off length for > ; the born radius calculation. > rlist = 1.6 > ; [steps] freq to update neighbor list > nstlist = 1 67,68c68,69 < ; infinite coloumb cut-off radius < rcoulomb = 0 --- > ; coloumb cutoff radius > rcoulomb = 1.6 76,77c77,78 < ; Infinite VsW cutoff radius. < rvdw = 0 --- > ; Increasing VdW cutoff to same as everything else. > rvdw = 1.6 144c145 < rgbradii = 0 --- > rgbradii = 1.6 The complete offending mdp file will follow. Also if there's anything stupid in here unrelated to my current problem, please let me know too :). ; 7.3.2 Preprocssing ; ------------------ ; Apply constaint to alpha carbon atoms in alpha-crystalline domain. define = -DALPHACRYST_POSRES -DCHIRRES ; 7.3.3 Run Control ; ----------------- ; group(s) for center of mass motion removal comm_grps = System ; Do Langevin dynamics. integrator = sd ; maximum number of steps to integrate nsteps = 100000000 ; remove center of mass translation and rotation around centre of mass comm_mode = Angular ; [ps] time step for integration dt = 0.002 ; [steps] frequency of mass motion removal nstcomm = 10 ; [ps] starting time for run tinit = 0 ; 7.3.4 Langevin Dynamics ; ----------------------- ; Use PID to seed random number. ld_seed = -1 ; 7.3.8 Output Control ; -------------------- ; [steps] freq to write velocities to trajectory nstvout = 0 ; [steps] freq to write energies to log file nstlog = 1000 ; [steps] freq to write energies to energy file nstenergy = 1000 ; group(s) to write to xtc trajectory xtc_grps = System ; [real] precision to write xtc trajectory xtc_precision = 1000 ; [steps] freq to write coordinates to xtc trajectory nstxtcout = 1000 ; [steps] freq to write coordinates to trajectory nstxout = 0 ; group(s) to write to energy file energygrps = System ; [steps] freq to write forces to trajectory nstfout = 0 ; 7.3.9 Neighbour Searching ; ------------------------- ; [nm] cut-off distance for the short-range neighbor list. ; Set to zero for infinite cut-off. rlist = 0 ; Recalculating pair-list is not necessary with an infinite cut-off nstlist = 0 ; method of updating neighbor list ns_type = grid ; no periodic boundary conditions pbc = no ; 7.3.10 Electrostatics ; --------------------- ; apply a cut-off to electostatic coulombtype = cut-off ; infinite coloumb cut-off radius rcoulomb = 0 ; 7.3.11 VdW ; ---------- ; Dispersion correction makes no sense without box size. DispCorr = no ; twin-range cut-off with rlist where rvdw >rlist vdwtype = cut-off ; Infinite VsW cutoff radius. rvdw = 0 ; 7.3.13 Ewald ; ------------ ; [nm] grid spacing for FFT grid when using PME fourierspacing = 0.12 ; relative strength of Ewald-shifted potential at rcoulomb ewald_rtol = 1e-05 ; interpolation order for PME, 4 cubic pme_order = 4 ; 7.3.14 Temperature Coupling ; --------------------------- ; Temperature. ref_t = 600.0 ; temperature coupling frequency nsttcouple = 1 ; Thermostat is already taken care of by langevin dynamics. tcoupl = no ; couple everything to same bath tc_grps = System ; [ps] time constant for coupling tau_t = 1 ; 7.3.15 Pressure Coupling ; ------------------------ ; [bar] reference pressure for coupling ref_p = 1.0 ; pressure coupling in x-y-z directions pcoupltype = isotropic ; [ps] time constant for coupling tau_p = 2.0 ; no pressure coupling if using generalized born pcoupl = no ; [bar^-1] compressibility compressibility = 4.5e-05 ; 7.3.17 Velocity Generation ; -------------------------- ; velocity generation turned off gen_vel = no ; 7.3.18 Bonds ; ------------ ; apply constraints to the start configuration continuation = yes ; All bonds are constraints constraints = allbonds ; [degrees] maximum angle that a bond can rotate before LINCS will complain lincs_warnangle = 30 ; highest order in the expansion of the contraint coupling matrix lincs_order = 4 ; number of iterations to correct for rotational lengthening lincs_iter = 1 ; LINear Constraint Solver constraint_algorithm = LINCS ; 7.3.22 NMR refinement (dihedral restraints not in manual) ; --------------------------------------------------------- ; scaling factor for force constant for dihedral constraints dihre-fc = 10 ; Set chirality and omega angle restraints. dihre = yes ; 7.3.27 Implicit Solvent ; ----------------------- ; The cutoff radius for calculating the Born radii (must be equal to rlist). rgbradii = 0 ; Use a Generalized Born Solvent implicit_solvent = GBSA ; Use the Onufriev-Bashford-Case method to calculate the Born radii gb_algorithm = OBC ; Dielectric constant for implicit solvent. ; Default is 80 but we use 78.5 for consistency with amber. gb_epsilon_solvent = 78.5 -- gmx-users mailing list [email protected] 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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