Aldo Segura wrote:
Dear gmx-users,
I completed a MD (10 ns) of my protein-membrane system. When I perform a
visual inspection (VMD) of md_0_1.gro file I observed a few water
molecules within the bilayer. In previous steps (e.g. equilibration)
this was not observed. Could be expected such behavior?
Membrane protein systems take a long time (tens of ns or maybe more) to
equilibrate, so some water may drift in and out during the initial few ns as
voids in the lipids open and close. Nothing to worry about, unless for some
reason they persist out past the expected equilibration time.
-Justin
Best regards,
*//*
*/============================== =========
Aldo Segura-Cabrera
Laboratorio de Bioinformática
Centro de Biotecnología Genómica
Instituto Politécnico Nacional
Blvd. Del Maestro esquina Elías Piña, 88710
Reynosa, Tamaulipas, México.
(899)9243627 ext. 87747
e-mail: [email protected] <mailto:[email protected]>; [email protected]
<mailto:[email protected]>
============================== ===========/*
--
========================================
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
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