Seem that there is no suggestion here. So I kindly ask again (especially
Amber people) if possible to clarify this issue. I wish to additionally ask
why don't we can use ASMD given in amber tutorial. I repeated this and
lipid tutorial successfully and found them feasible within reasonable
computational cost. What's the difference between ASMD and "z-constraint PMF
method"?
Will someone answer me please.
Cheers
Zoran
-----Original Message-----
From: zoran matovic
Sent: Saturday, February 6, 2016 2:32 PM
To: amber_list
Subject: [AMBER] Z-constraint PMF method
Dear Amber users,
I’ve red CJ Dickson’s thesis (web available) where he stated that
“z-constraint PMF method” is not suitable to be handled by sander nor pmemd
code. He worked on PET tracers permeability through lipid bilayer. This was
stated 2014. and I wonder if something has been done about this issue
meanwhile . If the progress has been done could someone help me about this
procedure (papers, tutorial,..). I am working with some metal containing
drugs and wish to evaluate their ability to diffuse across the membrane
layer.In my opinion it is by far best way to evaluate molecular dynamic
results using the same code.
Thanks in advance.
Cheers
Zoran
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Received on Sun Feb 07 2016 - 10:30:03 PST
