On 7/16/12 10:39 AM, Giovani Mancini wrote:
Dear Justin,
Thank you very much for your immediate response to my e-mail.
I am trying to conduct umbrella sampling simulations of a molecule into a lipid
bilayer (DLPC) along the z-axis. As a reference, I used your tutorial which is
well-written and provide useful information of how to set up the system in
GROMACS.
I'm glad you found it useful. You almost certainly want cylindrical restraints,
which are described in the manual, section 6.3 with corresponding Figure 6.2 to
illustrate its principles. The overall workflow is very similar to the
tutorial, but the contents of the .mdp files will be quite different.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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