[gmx-users] Re: Re: umbrella potential

[Stefan Hoorman]

>
>
>
> > 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 = 1.7;
> > 5250 = 1.62; 5500 = 1.6; 5750 = 1.73; 6000 = 1.85; 6250 = 1.86; 6500 =
> > 1.91; 6750 = 1.84; 7000 = 1.88; 7250 = 1.82; 7500 = 1.93 ; 7750 = 2.04;
> > 8000 = 2.16 ; 8250 = 2.3 ; 8500 = 2.32 ; 8750 = 2.45 ; 9000 = 2.52 ;
> > 9250 = 2.5 ; 9500 = 2.62 ; 9750 = 2.65 ; 10000 = 2.66
>
> There is substantial overlap and jumping back and forth (i.e., 1.56,
> decrease to
> 1.54, increase to 1.56, then back to 1.52, etc) in these distances, so I
> think
> they are not optimal for umbrella sampling.  Instead of more regular
> spacing in
> time, I would suggest more regular spacing in terms of distance.  Most
> literature on the topic cites how far apart windows were in terms of
> distance,
> which is important for WHAM analysis.
>
> -Justin
>
>
> Is there a way to do this automatically in gromacs? To extract structures
from the simulation based on the distance between them?
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