[gmx-users] .mdp file

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 10 13:54:14 CET 2008

Andrea Muntean wrote:
> Hello there,
> I have a practical question regarding the mdp file, regardless the
> system to simulate. Before I would run a md simulation, usually we
> have to run grompp in order to preprocess the system. So I obtain,
> among other files, the mdout.mdp, based on the input mdp file. My
> question:
> If I want to run another simulation, with the same input, only with
> small changes in the mdp file (like number of steps or so), do I have
> to each time modify the input .mdp and run grompp, or is it enough if
> I modify mdout.mdp?

No.  The mdout.mdp file is output, a record of all the simulation parameters, 
including the ones you accepted as defaults by not explicitly entering into your 
grompp.mdp file (the input).  If you want to run different simulations, you need 
  to modify your input, or else these new parameters will never reach the .tpr 
file and you will be running the same thing over and over again.


> Best regards,
> Andrea
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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