On 4/5/13 3:29 AM, Albert wrote:
Hello:
I am trying to do umbrella sampling for a protein/ligand water system these
days following Justin's nice tutorial. And I've got some questions:
(1) in the tutorial, the small peptide was pulling along Z direction. I am just
wondering, will the small peptide be pulled in both +Z and -Z direction?
In my case I've got a ligand in the deep pocket, it is possible that the ligand
can escape the binding pocket from two opposite site, let's say -Z and +Z which
I hope the umbrella sampling can give me some evidences to prove this.... Could
the umbrella sampling answer this question? Or we should pull the ligand along
X,Y and Z three direction so that it is more convinced?
The peptide is pulled/restrained in whatever direction you tell it. The
tutorial is just a simple example of the most trivial case, a one-dimensional
pull along an axis. You can do far more complex things using appropriate settings.
(2) it is said that when doing free energy calculation in gromacs, we'db better
use double precision Gromacs. So probably we have to use CPU instead of GPU for
this?
I don't think the pull code works on GPU (someone correct me if I'm wrong), but
in any case, I think the general reference to "free energy calculations" usually
just refers to alchemical transformations. In most cases with umbrella
sampling, your error bars will be orders of magnitude larger than any increase
in precision.
-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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