[gmx-users] distance VS. direction option in Umbrella sampling, in Gromacs 4.0

[Justin A. Lemkul]

DeChang Li wrote:
> Dear all,
>  
>     What is the difference between the option Distance and Direction in 
> Umbrella Sampling?
>     In my opinion, the option Direction means that pulling the 
> pull_group1 through the direction related to the reference group. Right? 
> But how about the option Distance?
> 

There was some discussion about this previously, so do search the archives.  If 
memory serves, "distance" does not allow negative relative displacements, while 
any of the other pull methods do.  The "distance" method is most applicable when 
pulling such that the COM distance always increases, or remains positive 
throughout the process.

Also, from an application perspective, the .mdp file options are different 
(direction + pull_vec1, distance + pull_dim).

-Justin

-- 
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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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