[gmx-users] doing simplest simulations
Mark.Abraham at anu.edu.au
Sat Aug 11 08:16:05 CEST 2007
Nicolas Schmidt wrote:
> Hi again,
> I re-did my simulations with the posted .mdp-file. The huge differences
> to my formerly posted file are a few vanished semicolons, and after a
> fine simulation-run an added dispersion correction due to a pressure
> that was slightly higher than expected. Did't really help, made it
> worse. But at least the simulations are now at the speed I expected them
> to be (gromacs doesen't scale that beautiful under my configuration, any
You're using default electrostatics and appear to have ignored the
advice I made last time about following some tutorial material. Are you
trying to generate random numbers and annoy people who might have some
interest in helping you? :-)
> Anyhow, two further questions:
> First: Is the configuration with r_list = r_vdw and nst_list = 1 a good
> choice, especially regarding speed? Suggestions?
Forget about speed until you get a decent model of physics working. Fast
and inaccurate is worse than worthless.
> (I caught a glimpse at the archives of this forum and couldn't quite
> find out why the radius of the neighbour-list has to be smaller than
> r_vdw, isn't that list something similar to the verlet-neighbour-lists?
> Shouldn't it therefore be bigger? But in this case I'm just curious...)
That's what the early manual chapters are for.
> Second: Am I simulating fixed connections?
> Are my chosen options on the
> .mdp-file therefor correct?
By comparison with what?
> Is gromacs doing as less as possible?
Que? We're trying to model ethane here. Try to minimize costs *after*
you achieve a model that works.
> sometimes at simulations with higher density complains 'bout
> constraints. Have I chosen the right configuration in the .itp-file?
That's what manual section 7.3 is for.
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