DeChang Li wrote:
------------------------------
Message: 2
Date: Tue, 16 Nov 2010 08:01:42 -0500
From: "Justin A. Lemkul" <[email protected] <mailto:[email protected]>>
Subject: Re: [gmx-users] distance VS. direction option in Umbrella
sampling, in Gromacs 4.0
To: Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
Message-ID: <[email protected] <mailto:[email protected]>>
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
========================================
--
========================================
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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