[gmx-users] Re: Re: umbrella potential

[Justin A. Lemkul]

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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