[gmx-users] Error while running protein-carbohydrate simulation
Deep Bhattacharya
hypergenetics at gmail.com
Mon Jul 11 02:25:01 CEST 2016
Evan,
It is a carbohydrate protein solvent complex that I am trying to simulate.
How do i check for the stabilization after the NVT and NPT equilibration?
Awaiting your response.
Sincerely,
Deep
On Sun, Jul 10, 2016 at 7:21 PM, Evan Lowry <evanwlowry at gmail.com> wrote:
> 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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--
Deep Bhattacharya.
Post-Graduate Student,
Department of Pharmaceutical Chemistry,
Bombay College Of Pharmacy.
Mobile - +918976129616
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