<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 16 Nov 2010 08:01:42 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] distance VS. direction option in Umbrella<br>
sampling, in Gromacs 4.0<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4CE280B6.2080007@vt.edu">4CE280B6.2080007@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
DeChang Li wrote:<br>
> Dear all,<br>
><br>
> What is the difference between the option Distance and Direction in<br>
> Umbrella Sampling?<br>
> In my opinion, the option Direction means that pulling the<br>
> pull_group1 through the direction related to the reference group. Right?<br>
> But how about the option Distance?<br>
><br>
<br>
There was some discussion about this previously, so do search the archives. If<br>
memory serves, "distance" does not allow negative relative displacements, while<br>
any of the other pull methods do. The "distance" method is most applicable when<br>
pulling such that the COM distance always increases, or remains positive<br>
throughout the process.<br>
<br>
Also, from an application perspective, the .mdp file options are different<br>
(direction + pull_vec1, distance + pull_dim).<br></blockquote><div><br></div><div> 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? </div>
<div> </div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br></blockquote></div>