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