[gmx-users] help and a tutorial

Sebastien Gerega seb at gerega.net
Wed Oct 12 05:25:58 CEST 2005

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 1.842 
which 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

Would anyone be able to help me with this error? and the MDS of this 
system (pdb file linked previously) in general?
I have been looking around for tutorials but the ones on the Gromacs 
website seem outdated as some of the links do not even work - are there 
any recommended tutorials online?

any help would be greatly appreciated thanks,

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