[gmx-users] Error while running protein-carbohydrate simulation
Deep Bhattacharya
hypergenetics at gmail.com
Mon Jul 11 01:00:14 CEST 2016
Thank you Evan for your response.
What time would you suggest for the coupling time for temperature and
pressure? Yes I will use the Nose-Hoover thermostat and see how the
simulation goes.
So you mean to change like this
; Temperature coupling =
tcoupl = nose-hoover
; Groups to couple separately =
tc-grps = PROTEIN SOL_Na
; Time constant (ps) and reference temperature (K) =
tau-t = 0.5 0.5
ref-t = 300 300
; Pressure coupling =
Pcoupl = parrinello-rahman
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau-p = 5.0
compressibility = 4.5E-5
ref-p = 1.0
Awaiting your response
Thank you.
Deep
On Sun, Jul 10, 2016 at 5:53 PM, Evan Lowry <evanwlowry at gmail.com> wrote:
> 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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--
Deep Bhattacharya.
Post-Graduate Student,
Department of Pharmaceutical Chemistry,
Bombay College Of Pharmacy.
Mobile - +918976129616
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