Nicolas Schmidt wrote:
Hi, I'm doing a comparison in the aspect of speed between gromacs and an
other MD-simulation-program, that isn't providing all the diffrent
options of gromacs.
My problem is, that the results I got from the simulations with gromacs
aren't reasonable. E.g negative pressure and zero kelvin or ridiculously
high pressure and temperature. The simulations are running more or less
fine (though they are too fast ;-) ), but if the results are rubbish I
can't say anything 'bout the speed at all...
I'm assuming your protocol sets up a system of bulk ethane with a
reasonable density, and that there were no warnings you overlooked.
Of course I'm assuming I did a terribly stupid mistake, so I'm asking
you to take a look at my files (added all necessary ones) and correct me
(they are less big than you might emagine, resulting from the pretty
simple molecules I'm buidling up)
Energy minimization before beginning equilibration MD is usually a good
idea. I've no idea why you think turning off basically the entire set of
.mdp options is a good idea, or why you're T-coupling at 183K. Since
you're new, I'd check out
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and
follow along some tutorial material, and then adapt a protocol and .mdp
file to your needs. Trying to measure temperature and pressure from a
single run that didn't have a pre-equilibration phase is just asking for
a crazy result.
Mark
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