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

[Quyen V. Vu]

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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