On Mon, Jan 9, 2012 at 3:46 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 10/01/2012 7:19 AM, Ben Reynwar wrote: > > On Tue, Dec 20, 2011 at 7:16 PM, Mark Abraham <mark.abra...@anu.edu.au> > 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 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 > > 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. > > > All that sounds very much like a bug. Please open an issue here > http://redmine.gromacs.org and attach the lowest four .tpr and .cpt input > files for the failing case. This will allow someone to find out why and > perhaps fix it. > > Mark > Done (http://redmine.gromacs.org/issues/860)
> > > 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 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 -- 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
