[gmx-users] Simulation crashed - Large VCM, Pressure scaling more than 1%, Bond length not finite
kevin.boyd at uconn.edu
Mon Feb 25 16:31:06 CET 2019
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.
On Mon, Feb 25, 2019 at 8:15 AM zeineb SI CHAIB <zeineb-14 at hotmail.com>
> 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
> 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
> 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
> 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
> 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.
> Gromacs Users mailing list
> * Please search the archive at
> before posting!
> * Can't post? Read
> * For (un)subscribe requests visit
> or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users