Stefan Hoorman wrote:
Well, I tried again, this time simulating 1ns each window. I thought
about simulating more, but thought of making a test before making longer
simulations for nothing. And again, my histogram looks like a
chromatographic peak, but the range this time is different. The re
> Stefan Hoorman wrote:
>
> > I simulate 400 ps for each window. I have a total of 20 windows. My
>
> 400 ps is relatively short, especially given the speed of current hardware
> and
> of Gromacs 4.0. I generally see longer time periods in the literature.
>
> > histogram looks like a chromatograph
Stefan Hoorman wrote:
I have a test set which is comprised of the same constituents of my real
system, except the solvent (i mean, it is in vacuum. This test set I use
to (as the name says) test different different parameters without having
to wait too much. I know it would not serve as a ve
>
>
> Stefan Hoorman wrote:
> >
> >
> > > The distances between the two structures in each of the windows
> > are (in nm):
> > > 0ps = 1.56 ; 500ps = 1.54; 1000ps = 1.56; 1500 = 1.56; 2000 =
> > 1.52; 2500
> > > = 1.65; 3000 = 1.66; 3500 = 1.77; 4000 = 1.63; 4500 = 1.62; 5000
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