[gmx-users] Simulation crashed, fatal error: Bond length not finite and warning: Pressure scaling more than 1%.

Kroon, P.C. p.c.kroon at rug.nl
Fri May 25 23:21:14 CEST 2018


You equilibrations are probably too short. There are some pretty slow
processes in lipid membranes.

Peter

On Fri, May 25, 2018 at 6:00 PM, Quyen V. Vu <vuqv.phys at gmail.com> wrote:

> Hi Zeined,
> Have you check the energy , the box fluctuations and pressure deviations ?
> Best,
> Quyen
>
>
>
> On Fri, May 25, 2018 at 6:30 PM, zeineb SI CHAIB <zeineb-14 at hotmail.com>
> wrote:
>
> > Dear GMX users,
> >
> >
> > I'm running a coarse-grained simulation of a homo-dimer in a membrane
> > composed of POPC, POPE, and CHOL (31%, 41%, 28% respectively), using
> > MARTINI force field and GROMACS software.
> >
> >
> > I followed the usual steps with 1ns minimization, 50 ns NVT equilibration
> > followed by 50ns NPT equilibration.
> >
> >
> > After running 2.5μs of simulation on a cluster, the system crashed with a
> > fatal error:
> >
> >
> > Step 108657121  Warning: Pressure scaling more than 1%. This may mean
> your
> > system is
> >
> > not yet equilibrated. Use of Parrinello-Rahman pressure coupling during
> >
> > equilibration can lead to simulation instability and is discouraged.
> >
> >
> > Fatal error:
> >
> > Bond length not finite.
> >
> >
> > When I analyzed the pressure and the temperature they seem OK. Pressure
> > average = 1.04 bar and Temperature average 314.835 K
> >
> >
> > I don't know what I'm missing and can't diagnose the problem.
> >
> >
> > Any help, please?
> >
> >
> > Thank you in advance for your help and consideration.
> >
> >
> >
> >
> > NB: I used the following MDP parameters for the production run (They are
> > the optimal parameters to run with MARTINI FF):
> >
> >
> > ; TIMESTEP IN MARTINI
> >
> > ; Most simulations are numerically stable with dt=40 fs,
> >
> > ; however better energy conservation is achieved using a
> >
> > ; 20-30 fs time step.
> >
> > ; Time steps smaller than 20 fs are not required unless specifically
> > stated in the itp file.
> >
> >
> > integrator              = md
> >
> > dt                            = 0.02
> >
> > nsteps                    = 50000000
> >
> >
> > nstxout                  = 100
> >
> > nstvout                  = 100
> >
> > nstfout                  = 0
> >
> > nstlog                    = 1000
> >
> > nstenergy                = 100
> >
> > nstxout-compressed       = 1000
> >
> > compressed-x-precision   = 100
> >
> >
> > continuation           = yes     ; Restarting after NPT
> >
> >
> > ; NEIGHBOR LIST and MARTINI
> >
> > ; To achieve faster simulations in combination with the Verlet-neighbor
> > list
> >
> > ; scheme, Martini can be simulated with a straight cutoff. In order to
> >
> > ; do so, the cutoff distance is reduced 1.1 nm.
> >
> > ; The Verlet neighbor list scheme will automatically choose a proper
> > neighbor list
> >
> > ; length, based on a energy drift tolerance.
> >
> > ;
> >
> > ; Coulomb interactions can alternatively be treated using a
> reaction-field,
> >
> > ; giving slightly better properties.
> >
> > ; Please realize that electrostatic interactions in the Martini model are
> >
> > ; not considered to be very accurate, to begin with, especially as the
> >
> > ; screening in the system is set to be uniform across the system with
> >
> > ; a screening constant of 15. When using PME, please make sure your
> >
> > ; system properties are still reasonable.
> >
> >
> > cutoff-scheme            = Verlet
> >
> > nstlist                  = 20
> >
> > ns_type                  = grid
> >
> > pbc                      = xyz
> >
> > verlet-buffer-tolerance  = 0.005
> >
> >
> > coulombtype              = reaction-field
> >
> > rcoulomb                 = 1.1
> >
> > epsilon_r                = 15 ; 2.5 (with polarizable water)
> >
> > epsilon_rf               = 0
> >
> > vdw_type                 = cutoff
> >
> > vdw-modifier             = Potential-shift-verlet
> >
> > rvdw                     = 1.1
> >
> >
> > ; MARTINI and TEMPERATURE/PRESSURE
> >
> > ; Good temperature control can be achieved with the V-rescale
> >
> > ; thermostat using a coupling constant of the order of 1 ps. Even better
> > ; temperature control can be achieved by reducing the temperature
> coupling
> >
> > ; constant to 0.1 ps, although with such tight coupling (approaching
> >
> > ; the time step) one can no longer speak of a weak-coupling scheme.
> >
> > ; We therefore recommend a coupling time constant of at least 0.5 ps.
> >
> > ; The Berendsen thermostat is less suited since it does not give
> >
> > ; a well described thermodynamic ensemble.
> >
> > ;
> >
> > ; Pressure can be controlled with the Parrinello-Rahman barostat,
> >
> > ; with a coupling constant in the range 4-8 ps and typical
> compressibility
> >
> > ; in the order of 10e-4 - 10e-5 bar-1. Note that, for equilibration
> > purposes,
> >
> > ; the Berendsen barostat probably gives better results, as the
> Parrinello-
> >
> > ; Rahman is prone to oscillating behaviour. For bilayer systems the
> > pressure
> >
> > ; coupling should be done semiisotropic.
> >
> >
> > tcoupl              = v-rescale
> >
> > tc-grps             = Protein POPC_POPE_CHOL W_ION
> >
> > tau_t               = 1.0  1.0 1.0
> >
> > ref_t               = 315 315 315  ;used in AA simulation
> >
> >
> > Pcoupl              = parrinello-rahman
> >
> > Pcoupltype          = semiisotropic
> >
> > tau_p               = 12.0 ; parrinello-rahman is more stable with larger
> > tau-p, DdJ, 20130422
> >
> > compressibility     = 3e-4  3e-4  3e-4
> >
> > ref_p               = 1.0  1.0  1.0
> >
> >
> > gen_vel             = no
> >
> > gen_temp            = 315
> >
> > gen_seed            = 473529
> >
> >
> > ; MARTINI and CONSTRAINTS
> >
> > ; for ring systems and stiff bonds constraints are defined
> >
> > ; which are best handled using Lincs.
> >
> >
> > constraints              = none
> >
> > constraint_algorithm     = Lincs
> >
> >
> > ; COM motion removal
> >
> > ; These options remove motion of the protein/bilayer relative to the
> > solvent/ions
> >
> > nstcomm        = 100
> >
> > comm-grps = Protein_POPC_POPE_CHOL W_ION
> >
> > --
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> >
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