[gmx-users] Error while running protein-carbohydrate simulation
Evan Lowry
evanwlowry at gmail.com
Mon Jul 11 02:21:36 CEST 2016
If it's just the carbohydrate in vacuum then 100ps may be fine. Check the
total energy and see If it is stabilizing in that time frame. If you have a
solvent then you should make the equilibration longer in my opinion. Hope
that helps.
Evan L.
On Jul 10, 2016 6:12 PM, "Deep Bhattacharya" <hypergenetics at gmail.com>
wrote:
> 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
> --
> Gromacs Users mailing list
>
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