[gmx-users] water molecule cannot be settled

MD refmac5 at gmail.com
Wed Nov 29 21:26:12 CET 2017


I was trying to minimize a solvated structure with following commands but I
got stuck at an error message complaining about water molecule not settled
when I was trying to 'gmx mdrun -v -deffnm em'.  I copied the grompp and
mdrun command, log file and the error message after the command. Any help
will be appreciated.

'gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr'

NOTE 1 [file em_real.mdp]:
  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
  that with the Verlet scheme, nstlist has no effect on the accuracy of
  your simulation.

Setting the LD random seed to 2057414563
Generated 97877 of the 97903 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 64492 of the 97903 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
Excluding 3 bonded neighbours molecule type 'Other_chain_B'
Excluding 3 bonded neighbours molecule type 'Protein_chain_C'
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 1 bonded neighbours molecule type 'NA'

NOTE 2 [file topol.top, line 53]:
  System has non-zero total charge: -0.859995
  Total charge should normally be an integer. See
  for discussion on how close it should be to an integer.

Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   345    Protein residues
There are:    14        Ion residues
There are:     1      Other residues
There are: 18022      Water residues
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting
into groups...
Number of degrees of freedom in T-Coupling group rest is 125097.00
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 80x80x80, spacing 0.119 0.119 0.119
Estimate for the relative computational load of the PME mesh part: 0.20
This run will generate roughly 5 Mb of data

There were 2 notes

'gmx mdrun -v -deffnm em'

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000

WARNING: Listed nonbonded interaction between particles 4630 and 4646
at distance 2.141 which is larger than the table limit 2.000 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.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

Step=    0, Dmax= 1.0e-02 nm, Epot=  1.37831e+08 Fmax= 2.33474e+10, atom=
Step=    1, Dmax= 1.0e-02 nm, Epot=  8.10627e+06 Fmax= 9.06678e+08, atom=
Step=    2, Dmax= 1.2e-02 nm, Epot=  1.57170e+06 Fmax= 5.63829e+07, atom=
Step=    3, Dmax= 1.4e-02 nm, Epot=  4.98801e+05 Fmax= 1.15297e+07, atom=
Step=    4, Dmax= 1.7e-02 nm, Epot=  2.84347e+05 Fmax= 2.00959e+06, atom=
Step=    5, Dmax= 2.1e-02 nm, Epot=  1.73937e+05 Fmax= 5.63524e+05, atom=
Step=    6, Dmax= 2.5e-02 nm, Epot=  8.01156e+04 Fmax= 5.40120e+05, atom=
Step=    7, Dmax= 3.0e-02 nm, Epot=  1.58428e+04 Fmax= 5.15983e+05, atom=
Step=    8, Dmax= 3.6e-02 nm, Epot= -4.53540e+04 Fmax= 4.90339e+05, atom=
Step=    9, Dmax= 4.3e-02 nm, Epot= -1.02816e+05 Fmax= 4.58354e+05, atom=
Step=   10, Dmax= 5.2e-02 nm, Epot= -1.54031e+05 Fmax= 4.23043e+05, atom=
Step=   11, Dmax= 6.2e-02 nm, Epot= -2.10519e+05 Fmax= 1.10326e+06, atom=
Step=   12, Dmax= 7.4e-02 nm, Epot= -2.22123e+05 Fmax= 3.74510e+05, atom=
Step=   13, Dmax= 8.9e-02 nm, Epot= -2.99577e+05 Fmax= 2.76027e+05, atom=
Step=   14, Dmax= 1.1e-01 nm, Epot= -3.65363e+05 Fmax= 6.32069e+05, atom=
Step=   16, Dmax= 6.4e-02 nm, Epot= -3.79471e+05 Fmax= 1.98011e+05, atom=
Step=   17, Dmax= 7.7e-02 nm, Epot= -4.21782e+05 Fmax= 1.09246e+05, atom=
Step=   18, Dmax= 9.2e-02 nm, Epot= -4.79158e+05 Fmax= 1.69343e+05, atom=
Step=   19, Dmax= 1.1e-01 nm, Epot= -4.92508e+05 Fmax= 3.68756e+05, atom=

Back Off! I just backed up step20b.pdb to ./#step20b.pdb.1#

Back Off! I just backed up step20c.pdb to ./#step20c.pdb.1#
Wrote pdb files with previous and current coordinates


integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0  ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep      = 0.01      ; Energy step size
nsteps = 50000   ; Maximum number of (minimization) steps to perform
energygrps = Protein ; Which energy group(s) to write to disk

; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist     = 1     ; Frequency to update the neighbor list and long range
cutoff-scheme   = Verlet
ns_type     = grid ; Method to determine neighbor list (simple, grid)
rlist     = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype     = PME ; Treatment of long range electrostatic interactions
rcoulomb     = 1.0 ; long range electrostatic cut-off
rvdw     = 1.0 ; long range Van der Waals cut-off
pbc         = xyz ; Periodic Boundary Conditions

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