[gmx-users] help and a tutorial

Erik Lindahl lindahl at sbc.su.se
Wed Oct 12 11:23:31 CEST 2005

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  
> 1.842 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

It's described in more detail here:




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