[gmx-users] file too big?

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 22 11:18:01 CEST 2003

On Tue, 2003-04-22 at 10:35, Anton Feenstra wrote:
> David wrote:
\> > 
> > Not everyone is simulating proteins in water... For many things you do
> > need to save more often. Even for proteins, if you'd want to study order
> > parameters, you need to save like every 100 fs.
>  From my perspective (which is admittedly limited, and indeed biased towards
> proteins in water), that falls under the 'very specific things' category...
> If you need 100fs time resolution, do you also need very long simulations?
> (i.e. <1ns, my feeling is you wouldn't...)
In some cases yes: for the protein order parameters, you want a number
for each individual NH group, and you have only one copy. Furthermore
you may want to distinguish internal and external motions...
You'll need very long simulations with short time resolution, and all
those in multiple copies of course...

Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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