[gmx-users] Error while running protein-carbohydrate simulation
Deep Bhattacharya
hypergenetics at gmail.com
Mon Jul 11 02:12:36 CEST 2016
Evan,
It is a protein-carbohydrate system consisting of 12 disaccharide units for
the carbohydrate. The protein is CD44 receptor. Does protein-carbohydrate
system demand different parameters?
Does this help in deciding the parameters?
Awaiting your earnest response.
Sincerely,
Deep
On Sun, Jul 10, 2016 at 7:09 PM, Evan Lowry <evanwlowry at gmail.com> wrote:
> Can you give me more details about the system? 100 ps is very short and may
> not be adequate.
>
> Evan L.
> On Jul 10, 2016 5:22 PM, "Deep Bhattacharya" <
> deep.bhattacharya1991 at gmail.com> wrote:
>
> > Evan,
> > One more question,
> > Do I also increase the equilibration time from 100ps to 200ps? Will that
> > help along with the 1fs time step?
> >
> > Sincerely,
> > Deep
> >
> > Sent from my iPhone
> >
> > > On 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
> > >>>> --
> > >>>> Gromacs Users mailing list
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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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