[gmx-users] Re: distance VS. direction option in Umbrella sampling, in Gromacs 4.0 (Justin A. Lemkul)
Justin A. Lemkul
jalemkul at vt.edu
Tue Nov 16 16:41:31 CET 2010
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.
> > 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
> (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 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
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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