[gmx-users] Error while running protein-carbohydrate simulation

Evan Lowry evanwlowry at gmail.com
Mon Jul 11 00:53:10 CEST 2016


Try running with a 1 fs time step in stead of 2 fs. Also view your
trajectory to see if anything is messed up. Try re-minimizing as well. If
that doesn't work, you could change the coupling time for the temperature
and pressure.

On another note, why not use the Nose-Hoover thermostat? It may be more
accurate for the energies in your system.

Best of luck,

Evan L.
On Jul 10, 2016 4:45 PM, "Deep Bhattacharya" <hypergenetics at gmail.com>
wrote:

> Hello,
> I am trying to simulate the system mentioned but its failing showing this
> error message,
> WARNING: Listed nonbonded interaction between particles 746 and 751
> at distance 3f which is larger than the table limit 3f nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
>
>
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.6.5
> Source code file: /util/src/gromacs/gromacs-4.6.5/src/mdlib/pme.c, line:
> 851
>
> Fatal error:
> 1 particles communicated to PME node 13 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension y.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "Jede der Scherben spiegelt das Licht" (Wir sind Helden)
>
> Error on node 13, will try to stop all the nodes
> Halting parallel program mdrun on CPU 13 out of 16
>
> gcq#330: "Jede der Scherben spiegelt das Licht" (Wir sind Helden)
>
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 13 in communicator MPI_COMM_WORLD
> with errorcode -1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 13 with PID 117399 on
> node c0323 exiting improperly. There are two reasons this could occur:
>
> 1. this process did not call "init" before exiting, but others in
> the job did. This can cause a job to hang indefinitely while it waits
> for all processes to call "init". By rule, if one process calls "init",
> then ALL processes must call "init" prior to termination.
>
> 2. this process called "init", but exited without calling "finalize".
> By rule, all processes that call "init" MUST call "finalize" prior to
> exiting or it will be considered an "abnormal termination"
>
> This may have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
>
> Here is my .mdp file
> title       = CD44 deHA_sulf_red complex MD simulation
> ; Run parameters
> integrator  = md        ; leap-frog integrator
> nsteps      = 5000000    ; 2 * 5000000 = 10000 ps (10 ns)
> dt          = 0.002     ; 2 fs
> ; Output control
> nstxout             = 50000         ; suppress .trr output
> nstvout             = 50000         ; suppress .trr output
> nstenergy           = 50000      ; save energies every 100.0 ps
> nstlog              = 50000      ; update log file every 100.0 ps
> compressed-x-grps   = System
> energygrps          = Protein LIG
> ; Bond parameters
> continuation    = yes           ; first dynamics run
> 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
> cutoff-scheme   = Verlet
> ns_type         = grid      ; search neighboring grid cells
> nstlist         = 10        ; 20 fs, largely irrelevant with Verlet
> rcoulomb        = 1.4       ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.4       ; 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
> tcoupl      = V-rescale                     ; modified Berendsen thermostat
> tc-grps     = Protein_LIG Water_and_ions    ; two coupling groups - more
> accurate
> tau_t       = 0.1   0.1                     ; time constant, in ps
> ref_t       = 300   300                     ; reference temperature, one
> for each group, in K
> ; Pressure coupling
> pcoupl      = Parrinello-Rahman             ; pressure coupling is on for
> 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        ; assign velocities from Maxwell distribution
>
> I have performed 100 ps NVT and NPT simulation before doing the MD run.
> Please help
>
>
>
>
>
> *Deep S Bhattacharya*
>
> *Graduate Research Assistant*
>
> Mohs Biomedical Imaging & Nanotechnology Group
>
> Pharmaceutical Sciences
>
> *University of Nebraska Medical Center*
>
> 4018 Eppley Science Hall  |  Omaha, NE 68198-6805
>
> office 402.559.4349  | cell 402.906.1640
>
> deep.bhattacharya at unmc.edu.deep.bhattacharya199@gmail.com
> --
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