Re: [gmx-users] npt error
On 2/4/13 5:19 AM, Rajalakshmi.C wrote: hi all, i am trying to simulate a polymer in 5.2 nm box using the gromacs45a3 forcefield. the system is highly concentrated with 3400 water molecules. i did energy minimization for 10ps and NVT, NPT simulations for 100 ps during NPT simulation i got the error message as "inner product between old and new vector is < 0.0 and water molecules starting at atom 3892 cannot be settled ,check for bad contacts, change the time scale" can anyone suggest solution for this . i could not find what the reason will be .i will be waiting for the answer http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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 listgmx-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] npt error
hi all, i am trying to simulate a polymer in 5.2 nm box using the gromacs45a3 forcefield. the system is highly concentrated with 3400 water molecules. i did energy minimization for 10ps and NVT, NPT simulations for 100 ps during NPT simulation i got the error message as "inner product between old and new vector is < 0.0 and water molecules starting at atom 3892 cannot be settled ,check for bad contacts, change the time scale" can anyone suggest solution for this . i could not find what the reason will be .i will be waiting for the answer thankyou -- with regards, Rajalakshmi Molecular Modelling & simulations lab IIT Madras chennai-36 -- Open WebMail Project (http://openwebmail.org) -- gmx-users mailing listgmx-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] NPT error
Hi: I am following the tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html the NVT step goes well, but the NPT always doesn't work. it said: Program mdrun_mpi_bg, VERSION 4.5.5 Source code file: ../../../src/mdlib/domdec.c, line: 2633 Fatal error: Step 2970: The domain decomposition grid has shifted too much in the Y-direction around cell 2 3 1 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "Ich Bin Ein Berliner" (J.F. Kennedy) Error on node 81, will try to stop all the nodes Halting parallel program mdrun_mpi_bg on CPU 81 out of 128 gcq#193: "Ich Bin Ein Berliner" (J.F. Kennedy) Abort(-1) on node 81 (rank 81 in comm 1140850688): application called MPI_Abort(MPI_COMM_WORLD, -1) - process 8 1 BE_MPI (ERROR): The error message in the job record is as follows: BE_MPI (ERROR): "killed with signal 6" here is my NPT.mdp file: title= OPLS Lysozyme NPT equilibration define= -DPOSRES; position restrain the protein ; Run parameters integrator= md; leap-frog integrator nsteps= 10; 2 * 10 = 200 ps dt= 0.002; 1 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps ; Bond parameters continuation= yes; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 300 300; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off ;warning refcoord_scaling = all The last option in npt.mdp file "refcoord_scaling = all" was added by myself otherwise there are some warnings. Does anybody have any advices? THX -- gmx-users mailing listgmx-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] NPT error
Hi: I am following the tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/07_equil2.html the nvt step goes well, but the NPT always doesn't work. it said: Program mdrun_mpi_bg, VERSION 4.5.5 Source code file: ../../../src/mdlib/domdec.c, line: 2633 Fatal error: Step 2970: The domain decomposition grid has shifted too much in the Y-direction around cell 2 3 1 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "Ich Bin Ein Berliner" (J.F. Kennedy) Error on node 81, will try to stop all the nodes Halting parallel program mdrun_mpi_bg on CPU 81 out of 128 gcq#193: "Ich Bin Ein Berliner" (J.F. Kennedy) Abort(-1) on node 81 (rank 81 in comm 1140850688): application called MPI_Abort(MPI_COMM_WORLD, -1) - process 8 1 BE_MPI (ERROR): The error message in the job record is as follows: BE_MPI (ERROR): "killed with signal 6" here is my NPT.mdp file: title= OPLS Lysozyme NPT equilibration define= -DPOSRES; position restrain the protein ; Run parameters integrator= md; leap-frog integrator nsteps= 10; 2 * 10 = 200 ps dt= 0.002; 1 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps ; Bond parameters continuation= yes; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cells nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.10.1; time constant, in ps ref_t= 300 300; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off ;warning refcoord_scaling = all -- gmx-users mailing listgmx-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
