[gmx-users] doing simplest simulations
Mark.Abraham at anu.edu.au
Thu Aug 9 20:43:12 CEST 2007
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
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.
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