[gmx-users] Simulation crashed, fatal error: Bond length not finite and warning: Pressure scaling more than 1%.
Kevin Boyd
kevin.boyd at uconn.edu
Sat May 26 00:03:12 CEST 2018
> You equilibrations are probably too short. There are some pretty slow
> processes in lipid membranes.
The original poster stated that the system crashed after microseconds
of simulation, so this is not the case.
The pressure fluctuation message could be a red herring, with a system
explosion being the real issue. Since A) it's Martini, and B) the
system ran successfully for quite a while, it could potentially be a
domain decomposition issue. Can you try running mdrun with -rdd 1.5,
and see if that works? I'm imagining a scenario where two particles
with bonded interactions drift too far apart between domain
decomposition steps. This SHOULD trigger a different error message,
but I've seen some weird behavior in similar circumstances with
Martini before, where two bonded beads end up on opposite sides of the
box and a system explosion results.
Kevin
On Fri, May 25, 2018 at 5:08 PM, Kroon, P.C. <p.c.kroon at rug.nl> wrote:
> 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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