Poojari, Chetan wrote:
Hi,
I am working on membrane protein.
In umbrella sampling tutorial.......we saw the pulling of the peptide A away
from peptide B.
I want to pull the peptide deep into the hydrophobic core of the bilayer from
outside (solvent environment).
Please can someone suggest me how to go about this.
The same principles as in the tutorial apply. Choose a reference group
(membrane), a pull group (peptide), and a pull direction. You'll have to
empirically adjust pull rate, force constant, etc to properly treat your system.
-Justin
Kind regards,
chetan.
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Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
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========================================
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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