[gmx-users] Re: distance VS. direction option in Umbrella sampling, in Gromacs 4.0 (Justin A. Lemkul)

[Justin A. Lemkul]

DeChang Li wrote:
> 
> 
> 
>     ------------------------------
> 
>     Message: 2
>     Date: Tue, 16 Nov 2010 08:01:42 -0500
>     From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>     Subject: Re: [gmx-users] distance VS. direction option in Umbrella
>            sampling,       in Gromacs 4.0
>     To: Discussion list for GROMACS users <gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>>
>     Message-ID: <4CE280B6.2080007 at vt.edu <mailto:4CE280B6.2080007 at vt.edu>>
>     Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
>     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).
> 
> 
>    Does mean that when using distance + pull_dim (if using pull_dim = Y 
> Y Y), the pull force vector is pointing from the reference group to the 
> pull group? 
>  

The direction of the actual movement is defined by the pull_rate, which can be 
negative (i.e., pull_group1 moves closer to pull_group0 rather than further 
away).  This works alright (I think) as long as the relative displacement 
between pull_group1 and pull_group0 remains > 0.

-Justin

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