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 [email protected]
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 [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
