On 5/3/13 2:21 PM, James Starlight wrote:
Couple extra question about umbrella
Does it possible to use Collective variable (eigenvector from EDA or NMA)
as the pulling coordinate?
Does it possible to use output from essential dynamics sampling (here I can
use EDS in targeted mode to pull my structure to the target conformation)
for the umbrella's NPT+MD. What the input data in the mdp files must be in
that case using CV?
The restraints implemented within the pull code are simply harmonic potentials
or rigid constraints along physical vectors. If you want more abstract versions
of umbrella sampling, that sounds like a task for something like PLUMED.
-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
