[gmx-users] output - em.gro looks very strange

MD refmac5 at gmail.com
Wed Dec 6 22:57:41 CET 2017

Hi Gromacs folks,

After fixing the non-even charge issues I met new problems when running
The grompp worked and mdrun em worked as well with warning, but I found the
output em.gro looks very strange with several amino acids stretched to the
other side of the box. I had the command followed with log file. Any help
would be greatly appreciated.

I looked at the distance between 4641 and 4657 in solv_ions.gro and it is
actually 11.354A. I am not quite sure about the warning message.



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

GROMACS:      gmx grompp, VERSION 5.1.2
Executable:   /usr/bin/gmx
Data prefix:  /usr
Command line:
  gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr

Ignoring obsolete mdp entry 'title'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#

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 2763204595 <(276)%20320-4595>
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'
Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are:   345    Protein residues
There are:    11        Ion residues
There are:     1      Other residues
There are: 18021      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 179214.00
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 was 1 note

Back Off! I just backed up em.tpr to ./#em.tpr.3#

*gmx mdrun -v -deffnm em*

Reading file em.tpr, VERSION 5.1.2 (single precision)
Using 1 MPI thread
Using 6 OpenMP threads

Back Off! I just backed up em.trr to ./#em.trr.2#

Back Off! I just backed up em.edr to ./#em.edr.2#

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

WARNING: Listed nonbonded interaction between particles 4641 and 4657
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.


title = Minimization ; Title of run

; Parameters describing what to do, when to stop and what to save
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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