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
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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