[gmx-users] analyze an md run

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Wed Jan 31 18:36:05 CET 2007


On Wednesday, 31. January 2007 16:35, Joern Lenz wrote:
> dear users,
> i have modelled a system containing a protein plus a DNA and water
> molecules. Now I am wondering, if it is possible to use s.th. like g_energy
> to plot the fluctuation of energy, temperature, pressure etc. only of the
> protein and the DNA and NOT with the water molecules. that is because i
> want to compare several simulation runs and their changes in energy, temp
> ... .
> Is there any option to do so ? I also have defined lots of index groups for
> distinguish between groups in the system.

Yes, it is.

After defining groups in your index file you have to add to your mdp file:

energygrps  = Name_from_your_index_file

You also have to add -n index_file.ndx to grompp and mdrun, after your run 
take a look into your energy file, all information about this should be added 

> So I would be very happy if you have a solution for my problem, thank you
> very much in advance and have a nice evening.
> greetings
> joern
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 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
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