minnale wrote:
HI users,
I have embedded protein in popc bilayer and ran the minimisation
succesfully , before going equilibration I would like to confirm one
thing that how to run the equilibration with on which system keep
position restrain?
1.we will keep position restrain on all the systems(-DPOSRES_PROTEIN,
-DPOSRES_LIPID, -DPOSRES_WATER) at a time ?
or 2. keep position resrain on each system at a time and
3.is it require to keep position restrain on water?
Could you tell me clearly pls
Thanks alot in advance
If you "equilibrate" your system with every element of it restrained, I
think you will accomplish absolutely nothing. Typical procedures for
membrane proteins involve equilibrating with restraints on the protein
only, allowing the lipids to pack around the protein.
-Justin
HSBC
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========================================
Justin A. Lemkul
Graduate Research Assistant
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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