[gmx-users] Simulation crashed - Large VCM, Pressure scaling more than 1%, Bond length not finite

[Kevin Boyd]

Hi,

Is this crash reproducible? In my experience, I sometimes get random
crashes with Martini deep into a simulation that don't happen again when
restarting from a checkpoint.

Kevin

On Mon, Feb 25, 2019 at 8:15 AM zeineb SI CHAIB <zeineb-14 at hotmail.com>
wrote:

> Dear GMX users,
>
> I am running a Coarse-Grained simulation using Martini Force Field. My
> system consists of a Protein inserted in a lipid bilayer containing POPC,
> POPE, and CHOL molecules, in the presence of Water and ions.
>
> I followed the conventional steps to prepare my system for the production
> run:
> 1- Generating Coarse-Grained structure and topology files
> 2- Insertion of the protein in the lipid bilayer
> 3- Adding neutralizing counterions
> 4- Energy minimization with backbone positions restraints for 1ns.
> 5- NVT equilibration with backbone positions restraints for 50 ns with
> v-rescale.
> 6- NPT equilibration with backbone positions restraints for 50 ns with
> Parrinello-Rahman barostat.
>
> The simulation runs for ~ 2 microseconds before crashing:
> Large VCM (group Protein_POPC_POPE_CHOL): 965789.43750, -1086946.50000,
> 135001.78125, Temp-cm:  9.21574e+14
> Large VCM(group W_ION): -396609.00000, 446514.28125, -55416.26953,
> Temp-cm:  2.38187e+13
>
> Step 123438101  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.
>
> Program: gmx mdrun, version 2018.3
> Source file: src/gromacs/mdlib/clincs.cpp (line 2252)
> Fatal error: Bond length not finite.
>
> I used the following parameters in the mdp file (They were recommended by
> Martini People):
> integrator               = md
> dt                             = 0.02
> nsteps                     = 500000000
>
> nstxout                   = 100
> nstvout                   = 100
> nstfout                    = 0
> nstlog                     = 1000
> nstenergy              = 100
> nstxout-compressed         = 1000
> compressed-x-precision   = 100
>
> continuation           = yes
>
> cutoff-scheme            = Verlet
> nstlist                           = 20
> ns_type                       = grid
> pbc                               = xyz
> verlet-buffer-tolerance     = 0.005
>
> coulombtype        = reaction-field
> rcoulomb              = 1.1
> epsilon_r              = 15
> epsilon_rf             = 0
> vdw_type             = cutoff
> vdw-modifier       = Potential-shift-verlet
> rvdw                      = 1.1
>
> tcoupl             = v-rescale
> tc-grps            = Protein POPC_POPE_CHOL W_ION
> tau_t               = 1.0  1.0 1.0
> ref_t                = 315 315 315
>
> Pcoupl                    = parrinello-rahman
> Pcoupltype            = semiisotropic
> tau_p                      = 12.0
> compressibility     = 3e-4  3e-4  3e-4
> ref_p                       = 1.0  1.0  1.0
>
> gen_vel                 = no
> gen_temp            = 315
> gen_seed             = 473529
>
> constraints                       = none
> constraint_algorithm     = Lincs
>
> nstcomm           = 100
> comm-grps       = Protein_POPC_POPE_CHOL W_ION
>
> I had a look on the GROMACS mailing list for similar problems and probable
> causes:
>
> In one post they said that the Large VCM might be related to an
> un-equilibrated system but in my case, the system was equilibrated for 50ns
> (NVT equilibration) and another 50ns for the NPT equilibration so I don't
> think that this is the case here.
>
> Another suggestion for the VCM thing is that it might be related to the
> force field and the topology. Since the last 5 residues of my protein have
> not been solved I thought that it's better to keep the actual C-terminal
> residue neutral. I would have liked to use the capping residues but they
> are not parameterized in Martini force field.  Maybe this is why the
> simulation is crashing? But it runs for more than 2 microseconds before it
> crashed!
> I would like to have your opinion about this point, please.
>
> The error message is really confusing and I can't really understand it :
> VCM/Pressure scaling more that 1%/Bond length not finite.
>
> I would really appreciate your help on this.
>
> Zeineb
>
>
>
>
> --
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