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

[DeChang Li]

> ------------------------------
>
> Message: 2
> Date: Tue, 16 Nov 2010 08:01:42 -0500
> From: "Justin A. Lemkul" <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>
> Message-ID: <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?



>
> -Justin
>
> --
> ========================================
>
> 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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