Quoting pol...@fh.huji.ac.il: Dear gromacs users,
my box dimensions are 368A and when I run the simulation with nsteps=1 it works fine. The mdp files used for minimization and post-em simulation are attached.
Thanks again for your help. Regina
Quoting chris.ne...@utoronto.ca:What are your initial box dimensions prior to em? Also, please copy and paste your .mdp options. Also, what happens when you run the same post-em simulation with nsteps=1 ?-- original message -- Dear all, I'm trying to run simulation of 30 proteins in water using the Martini force field. I used water.gro file in order to solvate the proteins. For minimization I used the em.mdp file published at Martini site (http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol parameter to 10 the system can't converge. So I used emtol 100 and then the system converged. I use it as an input for the simulation. The file can't be attached as it is too big nut I can send it if needed. However, the sumulation crushes when I'm trying to run MD using md.mdp also from the Martini site. I'm getting the following warnings and errors: Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported. Box (3x3): Box[ 0]={ nan, nan, nan} Box[ 1]={ nan, nan, nan} Box[ 2]={ nan, nan, nan} Can not fix pbc. Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported. Box (3x3): Box[ 0]={ nan, nan, nan} Box[ 1]={ nan, nan, nan} Box[ 2]={ nan, nan, nan} Can not fix pbc. Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported. Box (3x3): Box[ 0]={ nan, nan, nan} Box[ 1]={ nan, nan, nan} Box[ 2]={ nan, nan, nan} Can not fix pbc. Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported. Box (3x3): Box[ 0]={ nan, nan, nan} Box[ 1]={ nan, nan, nan} Box[ 2]={ nan, nan, nan} Can not fix pbc. Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported. Box (3x3): Box[ 0]={ nan, nan, nan} Box[ 1]={ nan, nan, nan} Box[ 2]={ nan, nan, nan} Can not fix pbc. Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported. Box (3x3): Box[ 0]={ nan, nan, nan} Box[ 1]={ nan, nan, nan} Box[ 2]={ nan, nan, nan} Can not fix pbc. ------------------------------------------------------- Program mdrun_mpi, VERSION 4.0.3 Source code file: nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. ------------------------------------------------------- "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead) Error on node 0, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 0 out of 8 gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0[cli_0]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0 ------------------------------------------------------- Program mdrun_mpi, VERSION 4.0.3 Source code file: nsgrid.c, line: 348 Fatal error: Number of grid cells is zero. Probably the system and box collapsed. ------------------------------------------------------- Error on node 1, will try to stop all the nodes Halting parallel program mdrun_mpi on CPU 1 out of 8 gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3[cli_3]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3 gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5[cli_5]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5 gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4[cli_4]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4 gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6[cli_6]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6 gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2[cli_2]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2 gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead) application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1[cli_1]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1 When I looked at the pdb file attached I see something strange that is happening at the edges of the box. I can't understand what is the problem. Can someone help me with it? Thank you in advance. Regina ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ---------------------------------------------------------------- -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-usersPlease 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 thewww interface or send it to gmx-users-requ...@gromacs.org.Can't post? Read http://www.gromacs.org/Support/Mailing_Lists---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.
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; ; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0 ; ; for use with GROMACS 3.3 ; ; VARIOUS PREPROCESSING OPTIONS = title = Martini cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS = ; MARTINI - Most simulations are stable with dt=40 fs, ; some (especially rings) require 20-30 fs. ; The range of time steps used for parametrization ; is 20-40 fs, using smaller time steps is therefore not recommended. integrator = steep ; start time and timestep in ps tinit = 0.0 dt = 0.025 nsteps = 1000000 ; number of steps for center of mass motion removal = nstcomm = 1 comm-grps = ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 5000 nstvout = 5000 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 1000 nstenergy = 1000 ; Output frequency and precision for xtc file = nstxtcout = 1000 xtc_precision = 100 ; 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 = ; MARTINI - no need for more frequent updates ; or larger neighborlist cut-off due ; to the use of shifted potential energy functions. ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; MARTINI - vdw and electrostatic interactions are used ; in their shifted forms. Changing to other types of ; electrostatics will affect the general performance of ; the model. ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths = rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; MARTINI - normal temperature and pressure coupling schemes ; can be used. It is recommended to couple individual groups ; in your system seperately. ; Temperature coupling = tcoupl = no Pcoupl = no ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 320 gen_seed = 473529 ; OPTIONS FOR BONDS = ; MARTINI - for ring systems constraints are defined ; which are best handled using Lincs. constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 30 emtol = 10
; VARIOUS PREPROCESSING OPTIONS = title = Martini cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit = 0.0 dt = 0.030 nsteps = 1000000 ; number of steps for center of mass motion removal = nstcomm = 1 ; Groups for center of mass motion removal comm-grps = System ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 100 nstvout = 100 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 100 nstenergy = 100 ; Output frequency and precision for xtc file = nstxtcout = 100 xtc_precision = 100 ; 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 = Protein_PSE W_ION ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = Shift rcoulomb_switch = 0.0 rcoulomb = 1.2 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 15 ; Method for doing Van der Waals = vdw_type = Shift ; cut-off lengths = rvdw_switch = 0.9 rvdw = 1.2 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = Berendsen ; Groups to couple separately = tc-grps = Protein_PSE W_ION ; Time constant (ps) and reference temperature (K) = tau_t = 1.0 1.0 ref_t = 300 300 ; Pressure coupling = Pcoupl = berendsen Pcoupltype = isotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 1.0 1.0 compressibility = 5e-5 ref_p = 1.0 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 300 gen_seed = 473529 ; OPTIONS FOR BONDS = constraints = none ; Type of constraint algorithm = constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Highest order in the expansion of the constraint coupling matrix = lincs_order = 4 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs_warnangle = 30
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