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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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