[gmx-users] doing simplest simulations

Mark Abraham 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 
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.


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