XUEMING TANG wrote:
Hi there
I put a SDS Spherical micelle in solution and want to apply position
restraint before mdrun. Here I have a question: For macromolecules like
micelles, should the position restraint apply to not only the water
molecules (and ions) but also to the surfactant molecules in the
micelle? If it is also for the surfactant molecules, how to calculate
the position restraint time in this case.
Why would you restrain the solvent? That basically prevents equilibration from
happening. Then, if you restrain the solvent and surfactant, you truly
accomplish nothing.
Likely the best course of action is to restrain the surfactant molecules, while
allowing everything else to move freely. Then, remove all restraints and
equilibrate a while longer.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
