[gmx-users] Segmentation fault after warning regarding Listed nonbonded interaction
vivek sinha
viveksinha20002 at gmail.com
Thu Jul 17 17:58:23 CEST 2014
Hey Alex,
I was also having the same error from two days although my topology files
and mdp files were (I think) correct. Just two hours ago I corrected the
problem. I just changed the timestep from 0.002 to 0.0002 and it worked.
You can also try this.
Regards,
Vivek Sinha
On Fri, Jul 18, 2014 at 12:42 AM, Alexandre Barrozo <barrozo.ah at gmail.com>
wrote:
> Hi everybody,
>
>
> I am trying to make a simulation of an enzyme containing a metal ion using
> a dummy model for it. I have inserted all the parameters, generated the
> topology, solvated the system, without any problem.
>
> When I try to run a first equilibration, I get the following warning:
>
>
>
> WARNING: Listed nonbonded interaction between particles 127 and 134*
> at distance 3f which is larger than the table limit 3f nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> *These particles are close to the dummy model for the metal. I believe the
> problem might be related to that, but I had no problem in generating
> topologies, or anything like that.
>
>
> After that warning, I have a Segmentation fault.
>
>
> Here is my mdp file for the test equilibration that I was trying:
>
> define = -DPOSRES -DPOSRES_WATER ; position restrain
> the protein
> ; Run parameters
> integrator = md ; leap-frog
> integrator
> nsteps = 50000 ; 2 * 50000 = 100
> ps
> dt = 0.001 ; 1 fs
> ; Output control
> nstxout = 500 ; save coordinates
> every 1.0 ps
> nstvout = 500 ; save velocities
> every 1.0 ps
> nstenergy = 500 ; save energies
> every 1.0 ps
> nstlog = 500 ; update log file
> every 1.0 ps
> ; Bond parameters
> continuation = no ; first dynamics
> run
> ; constraint_algorithm = lincs ; holonomic
> constraints
> constraints = none ; all bonds (even
> heavy atom-H bonds) constrained
> ; Neighborsearching
> cutoff-scheme = Verlet
> ns_type = grid ; search
> neighboring grid cells
> nstlist = 30 ; 20 fs, largely
> irrelevant with Verlet
> rcoulomb = 1.0 ; short-range
> electrostatic cutoff (in nm)
> rvdw = 1.0 ; short-range van
> der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = PME ; Particle Mesh
> Ewald for long-range electrostatics
> pme_order = 4 ; cubic
> interpolation
> fourierspacing = 0.16 ; grid spacing for
> FFT
> ; Temperature coupling is on
> tcoupl = V-rescale ; modified
> Berendsen thermostat
> tc-grps = Protein Non-Protein ; two coupling
> groups - more accurate
> tau_t = 0.1 0.1 ; time constant, in
> ps
> ref_t = 1 1 ; reference
> temperature, one for each group, in K
> ; Pressure coupling is off
> pcoupl = no ; no pressure
> coupling in NVT
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = EnerPres ; account for
> cut-off vdW scheme
> ; Velocity generation
> gen_vel = yes ; assign velocities
> from Maxwell distribution
> gen_temp = 1 ; temperature for
> Maxwell distribution
> gen_seed = -1 ; generate a random
> seed
>
>
>
> Any clue about what is going on?
>
>
> Cheers,
>
> Alex
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