Steven Neumann wrote:
Dear Gmx Users,
Is it always required to restrained positions of the protein while
pulling your ligand? My system is made of 10 ligands attached to my
protein surface. I am pulling one of them.
No, it is not required. I assume you've gotten this idea from my tutorial - the
restraints there were used for a very specific purpose (detailed in the paper
linked from the tutorial).
I have just seen trajectory of pulling my ligand without restraining
positions of protein and 9 remaining ligands. My ligand while pulling
also pulled the protein with itself (for 1 nm distance) and then
splited. Is is this approach more reliable?
If your goal is umbrella sampling, you need only generate a series of reasonable
starting configurations along a defined reaction coordinate. The absolute
positions are irrelevant; it is the relative distance that matters.
-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
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