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

[Tsjerk Wassenaar]

Hi Andrew,

> I'm doing this tutorial:
> https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf
> 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.

Your observation is correct: it is a very small step.

> Is it ok or I need to clean up the warnings like in error below(it's for dt=0.002):

You probably know the answer already and I don't see the use of
answering this question. But obviously, you can't continue with such
errors. The following hints that something is very, very wrong. It's
hard to tell what it is as you don't give any command lines.
Apparently there are two bonded atoms that are at a distance of 2.6
nm! One thing that I can think of is that you used the output from
trjconv for further setting up of the simulation. These steps in the
tutorial are only for visualization of the simulation cell. You should
take the output from genbox (solvated.gro) and use it as input to
grompp. If this is a wrong diagnosis of your error, please provide
more information on what you did.

Cheers,

Tsjerk

>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623