[gmx-users] Question about umbrella sampling "pull-geometry" option

[Justin A. Lemkul]

WU Yanbin wrote:
> Dear GMXers,
> 
> I'm running umbrella PMF calculations using GROMACS 4.5. A molecule is 
> placed at various locations of a channel to compute the energy barrier 
> of the entrance.
> 
> Below is the PMF section of mdp input, to compute the PMF around the 
> position of (4.04700, 4.0582, -2.2058). The pulling molecule is 
> initially placed close to the (4.04700, 4.0582, -2.2058) position.
> The box size is 8.094*8.1164*6.0. The series of positions I considered 
> is in the z-coordinate range of -2.2 to -0.8.
> 
> -----------------------
> pull            = umbrella
> pull_geometry   = position
> pull_dim        = N N Y
> pull_start      = no      
> pull_ngroups    = 1
> pull_group0     =
> pull_group1     = MOL1
> pull_init1      = 4.04700  4.05820   -2.2058
> pull_rate1      = 0.00  
> pull_k1         = 1000  
> pull_nstxout    = 1000
> pull_nstfout    = 1000
> -----------------------
> 
> For this particular configuration, should I use "pull-geometry=position" 
> or "pull-geometry=distance"? Or they are the same for this case?
> I read the manual and PMF tutorial but cannot figure this out. Could 
> anyone provide more details about this?
> 

The "distance" method won't work.  Have you seen the following:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05a_pull_tips.html

To pull something through a channel, either "position" or "direction" should be 
able to do it.

-Justin

> Thank you.
> 
> Best,
> Yanbin
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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