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. Best regards Grigoris ----- Αρχικό μήνυμα ----- Απο: Justin Lemkul <jalem...@vt.edu> Προς: Giovani Mancini <giovani_m...@yahoo.gr>; Discussion list for GROMACS users <gmx-users@gromacs.org> Κοιν.: Στάλθηκε: 5:29 μ.μ. Δευτέρα, 16 Ιουλίου 2012 Θεμα: Re: [gmx-users] umbrella sampling On 7/16/12 10:25 AM, Giovani Mancini wrote: > Dear Gromacs users, > > I just read the tutorial by Justin Lemkul about umbrella sampling simulations > along z-axis. My question is whether we need cylindrical confinement of the > molecule that is pulling away from a reference molecule. > Thanks in advance > The tutorial is a very simple system designed to get users familiar with a basic workflow. There are more elegant ways of doing umbrella sampling for more complicated systems. Cylindrical restraints can be useful in some cases and are discussed in the manual. Without knowing more about the system you're considering, it's hard to provide specific advice. -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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
