Dear AMBER developers,
I’m interested in working with Lipid membrane simulation and
have recently read your interesting Soft Matter paper about GAFFlipid and I have
some quick questions:
1-Did
you simulate this in conjunction with a membrane protein like GPCR’s to see the
effect.?
2-I
have downloaded the parameters to play around with, the membrane does not have
holes, is it a good idea to insert it manually then let the system equilibrate with
time by minimization.?
3-As
I can understand, you simulate in a normal Periodic Boundary Conditions not in
the 2D phase space, is it true, if I understand it right, is it physically
sensible to do membrane simulation in 3D
space.?
4-Any
plan to include this in the normal Lipid11 forcefield soon, or I need to use
the coordinates and the parameters supplied for now.?
Full
of respect
Marawan
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Received on Sun Apr 07 2013 - 21:00:02 PDT
