[gmx-users] help and a tutorial

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Oct 12 13:45:08 CEST 2005

Hi Sebastien,

We meet again :)
For a general tutorial on MD you can walk through the one at
There is another one specifically on setting up systems of a protein and
ligand, which may also be interesting to you, but for these I don't know the
If you meet any problems directly related to the tutorial, you can also
contact me, as I'm for the greater part responsible for that site (and I
really need to revise it ;)).

The 1-4 interaction either means that you have overlaps due to the docking
process which cause the system to explode, or a faulty topology. If the
latter is the case you would probably have had a 'long bond' warning when
running grompp.



On 10/12/05, Erik Lindahl <lindahl at sbc.su.se> wrote:
> Hi Sebastien,
> On Oct 12, 2005, at 5:25 AM, Sebastien Gerega wrote:
> Hi all,
> I am pretty new to Gromacs and MDS in general... I am trying to run a
> simulation on a docked system (
> http://www.members.optushome.com.au/sebkg/test.pdb) and have tried several
> variations of what seem to be pretty standard settings to me but when I go
> to run the EM I get the following:
> step 0 warning: 1-4 interaction between 725 and 730 at a distance 1.842which is larger than the 1-4 table size
> 1.000 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
> Step 1 Warning: pressure scaling more than 1%, mu: 1.02036 1.02036 1.02036
> Segmentation fault
> It's described in more detail here:
> http://www.gromacs.org/faq/index.php#1-4cut
> Cheers,
> Erik
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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