Dear Gromacs users, I'm currently working with organic molecular solids and I'm trying to follow the protocol stablished in JCP, 139, 034104 (2013) (DOI: 10.1063/1.4812362). Before a production run in the NVT ensemble to get the Helmholtz potential for a certain molecular solid, I have to get the equilibrium box shape of the crystal I have under a certain pressure. I understand I have to use the anisotropic Parrinello-Rahman pressure coupling method for this purpose, but I'm facing some problems.
Some important information before stating the problem: 1. The initial coordinates are already at the minimum energy configuration. Each atom is bound to its lattice position by a harmonic potential and the initial structure corresponds to a minimum. No charge and vdw terms. 2. A NVT equilibration run works perfectly, with no warnings. After the submission of the job, when it reaches the NPT simulation the following error message is printed out: Fatal error: Not enough memory. Failed to realloc -201365740 bytes for grid->nra, grid->nra=0x6eff2010 (called from file /work/cluster/nate/GROMACS/gromacs-4.6.3/src/mdlib/nsgrid.c, line 492) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please notice that there is a negative number of bytes and that was new to me. Changing to the Berendsen barostat I got: Step 5 Warning: pressure scaling more than 1%, mu: 0.999968 1.00001 0.986164 Step 7 Warning: pressure scaling more than 1%, mu: 1.00043 0.999709 1.57535 Step 8 Warning: pressure scaling more than 1%, mu: 1.00144 0.999821 1.30892 Step 9 Warning: pressure scaling more than 1%, mu: 0.996529 1.00488 -18.9981 The job then would be killed because it exceeded the time it was allowed to run. Increasing tau_p here produced the same negative memory reallocation problem. My original mdp file is: integrator = md ; tinit = 0 ; dt = 0.002 ; nsteps = 100000 ; comm-mode = none ; ; Output Control nstxout = 5000 nstvout = 5000 nstfout = 5000 ; Output frequency for energies to log file and energy file nstlog = 1000 ; Output frequency and precision for xtc file nstxtcout = 1000 xtc-precision = 10000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 1 ; 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 = 1.0 ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions ; Method for doing electrostatics ;coulombtype = PME coulombtype = cut-off rcoulomb = 1.0 ; Method for doing Van der Waals vdw-type = cut-off ; cut-off lengths rvdw-switch = 1.0 rvdw = 1.0 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = AllEnerPres ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling Tcoupl = v-rescale tau_t = 2 ref_t = 298.15 tc-grps = system ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = anisotropic tau_p = 10 10 10 10 10 10 compressibility = 4.5e-05 4.5e-05 4.5e-05 4.5e-05 4.5e-05 4.5e-05 ref_p = 1.01325 1.01325 1.01325 1.01325 1.01325 1.01325 refcoord_scaling = com ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel = no gen_temp = 298.15 gen_seed = 3414125 ; Constraints constraints = all-angles constraint-algorithm = lincs lincs-iter = 4 lincs-order = 6 I'm relatively new to this kind of simulation and it would be really nice if someone helped me with it. Thank you very much! ~ Guilherme ***************************************************** Guilherme D. R. Matos Graduate Student at UC Irvine Mobley Group ***************************************************** -- 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.
