[gmx-users] Error while running protein-carbohydrate simulation
Deep Bhattacharya
hypergenetics at gmail.com
Mon Jul 11 01:13:26 CEST 2016
Thank you, Evan for your assistance.
I shall set the tau values as you suggested.
Yes I looking for calculation of energies after my simulation is complete
successfully.
I will reduce the time step and make changes in the algorithm as you have
suggested.
Thank you very much for your help.
Sincerely,
Deep
On Sun, Jul 10, 2016 at 6:09 PM, Evan Lowry <evanwlowry at gmail.com> wrote:
> I usually set tau-t=2.0 and tau-p=6.0 for most of my bulk fluid systems.
> It really depends on what you are simulating so just be sure to check the
> temperature and pressure to ensure that they are remaining constant and
> within your desired tolerances.
>
> I think you may have to change your pressure algorithm to Berendsen if you
> are using the Nose-Hoover thermostat, but definitely read about that in the
> gromacs manual. Nose-Hoover usually produces an accurate thermodynamic
> ensemble which is valuable if you are doing anything with energies.
>
> Evan L.
> On Jul 10, 2016 5:00 PM, "Deep Bhattacharya" <hypergenetics at gmail.com>
> wrote:
>
> > 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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--
Deep Bhattacharya.
Post-Graduate Student,
Department of Pharmaceutical Chemistry,
Bombay College Of Pharmacy.
Mobile - +918976129616
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