[gmx-users] Re: Re: Re: umbrella potential

[Stefan Hoorman]

>
>
> 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
> >     = 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?
> >
> >
>
> No, but you can use a script that iteratively calls g_dist on separate
> structures from your trajectory (trjconv -sep).  See, for example:
>
> http://oldwiki.gromacs.org/index.php/Making_Commands_Non-Interactive
>
> -Justin
>
>
> 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 very quantitative set, but
even though, when I changed the force_constant of the umbrella potentia to a
lower value (from 35 to 10) I got something out of the WHAM that looked more
like a "rollercoaster", I little bit edgy perhaps, but at least not a
downstream line like the one before. When I changed it again to 5 kJ, the
graphic still looked like a rollercoaster but it differed in 1 or 2 kcal
more negative than the one with 10 kJ as umbrella force constant. Perhaps,
in addition to space my intervals as a function of distance, my spring
constant is wrong. Does that make any sense?
Ahh...by the way, the link for oldwiki is not working. I will try it later.
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