Hi Justin, I was not able to find relevant posts in the archive. Any special keyword for searching?
But I wonder if it would introduce any additional error to deltaG calculations if I restrain the dissociation pathway to x axis, using pull_vecl = 1 0 0. Would the program then forcing the velocities along y and z axes to be zero? Thanks, Yun On Wed, Feb 20, 2013 at 5:16 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/20/13 1:14 AM, Yun Shi wrote: >> >> Hi all, >> >> For the purpose of calculating deltaG from umbrella sampling, I have >> first pulled my ligand away from the enzyme active site along an >> arbitrary direction (say x axis), setting the enzyme as pull_group0. >> >> But I found the ligand was moving in the yz plane while pulling along >> x, which I guess is not uncommon. Then I wonder which distance to use >> a reference for the definition of umbrella sampling windows. Would >> that be better to stick to the x component of protein-ligand distance, >> which I can easily read from pullx.xvg file while ignoring the y and z >> components? Or is it still better to use g_dist to calculate the >> absolute protein-ligand COM distance and use it for spacing reference? >> > > If you have motion in all three spatial dimensions, I would think that > ignoring deviations in any of them is inappropriate. Single-dimension > reaction coordinates only make sense if the desired path is linear along one > axis. If you're pulling something out of a binding cavity or channel that > is not exactly linear, that complicates matters. There were some nice > explanations of practical considerations for such simulations a few months > ago, so do check the archive. > > -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 > * 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
