[gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

NISHA Prakash nishnith20591 at gmail.com
Tue Dec 15 14:42:20 CET 2015

Hi all,

I am trying to simulate a protein using similar parameters as in the
tutorial - Protein ligand by Justin Lemkul.

I am facing a problem wherein the protein simulation is exploding only in
this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4.

The warning message is as follows

There were 4 inconsistent shifts. Check your topology

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

WARNING: Listed nonbonded interaction between particles 1312 and 1315
at distance 4.728 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.
ATOM   1312  O   TYR A 207
ATOM   1315  CD1 TYR A 207

em_real.mdp file

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


The initial minimization step itself fails.
I have tried to simulate a minimized structure as well, I still encounter
the same problem.

I would appreciate any help in this regard.
I would also like to know if this means, that the results from the older
version of gromacs reliable?

Thanking you in anticipation


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