[gmx-users] Isn't dt=0.0001 very small?

Andrew Voronkov drugdesign at yandex.ru
Tue Mar 10 08:36:13 CET 2009

Dear GROMACS users,
I'm doing this tutorial:
and I have an error with dt=0.002 or even dt=0.001 in pr.mdp during equilibration. It works only with dt=0.0001 which seems very very small step for me. Is it ok or I need to clean up the warnings like in error below(it's for dt=0.002):

starting mdrun 'T4-*LYPOZYME in water'
25000 steps,     50.0 ps.
Warning: 1-4 interaction between 2 and 20 at distance 2.619 which is larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

t = 0.000 ps: Water molecule starting at atom 100062 can not be settled.
Check for bad contacts and/or reduce the timestep.

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
Wrote pdb files with previous and current coordinates
step 0Segmentation fault
andrew at linux-f29d:~/GROMACS_MD/1LYD> 

Here is pr.mdp:

integrator = md
nsteps = 25000
dt = 0.001
nstlist = 10
rlist = 1.0
coulombtype = pme
rcoulomb = 1.0
vdw-type = cut-off
rvdw = 1.0
tcoupl = Berendsen
tc-grps = protein non-protein
tau-t = 0.1 0.1
ref-t = 298 298
Pcoupl = Berendsen
tau-p = 1.0
compressibility = 5e-5 5e-5 5e-5 0 0 0
ref-p = 1.0
nstenergy = 100
define = -DPOSRES

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