[gmx-users] problem with tutorial KALP-15 in DPPC

[tarak karmakar]

step 0: Water molecule starting at atom 101831 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.


I would suggest you to do one more round of minimization by taking the
final minimized .gro file and then perform a short simulation with a time
step of 0.5 fs. without any constraints.


cheers,
Tarak

On Mon, Feb 3, 2014 at 10:40 PM, serena <free882 at inwind.it> wrote:

> Hi all
> I'm doing the GROMACS tutorial KALP-15 in DPPC. I've done the steps until
> the energy minimization, so now I've my system at an energy minimum and
>  I'm
> doing the equilibration with this nvt.mdp:
>
> define          = -DPOSRES  ; position restrain the protein and lipid
> ; Run parameters
> integrator      = md            ; leap-frog integrator
> nsteps          = 50000         ; 2 * 50000 = 100 ps
> dt              = 0.002         ; 2 fs
> ; Output control
> nstxout         = 100           ; save coordinates every 0.2 ps
> nstvout         = 100           ; save velocities every 0.2 ps
> nstenergy               = 100           ; save energies every 0.2 ps
> nstlog          = 100           ; update log file every 0.2 ps
> ; Bond parameters
> continuation     = no                   ; first dynamics run
>  constraint_algorithm = lincs   ; holonomic constraints
>  constraints    = h-bonds               ; vecchio all bonds (even heavy
> atom-H bonds)
> constrained
>  lincs_iter     = 1                         ; accuracy of LINCS
>  lincs_order    = 4                         ; also related to accuracy
> ; Neighborsearching
> ns_type         = grid          ; search neighboring grid cels
> nstlist         = 5                 ; 10 fs
> rlist           = 1.2           ; vecchio: 1.0 short-range neighborlist
> cutoff (in nm)
> rcoulomb        = 1.2           ; short-range electrostatic cutoff (in nm)
> rvdw            = 1.2           ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype     = PME           ; Particle Mesh Ewald for long-range
> electrostat
> 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 DPPC SOL_CL   ; three coupling groups - more
> accurate
> tau_t           = 0.1   0.1     0.1             ; time constant, in ps
> ref_t           = 323   323     323             ; 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        = 323           ; temperature for Maxwell distribution
> gen_seed        = -1            ; generate a random seed
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the
> solvent/ions
> nstcomm         = 1
> comm-mode       = Linear
> comm-grps       = Protein_DPPC SOL_CL
>
> I've done this command:
> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
> mdrun -deffnm nvt
>
> but I received this error:
> starting mdrun 'Protein in water'
> 50000 steps,    100.0 ps.
>
> step 0: Water molecule starting at atom 101831 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> step 0: Water molecule starting at atom 99524 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> Wrote pdb files with previous and current coordinates
>
> Fatal error:
> 1 particles communicated to PME node 8 are more than 2/3 times the cut-off
> out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
>
> What means of this error? How to fix it?
> thank you
>
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/problem-with-tutorial-KALP-15-in-DPPC-tp5014235.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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