[gmx-users] doing simplest simulations

Mark Abraham 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 
> suggestions???).

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.

> Got 
> 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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