Dear Amber user group,
I am an undergraduate student in the Grabe and DeGrado labs at UCSF, and I
had a question concerning lipid simulations. I am attempting to closely
mirror the simulations carried out by Klauda and co-workers (Klauda, J.B.
et al.; J. Phys. Chem. B, 2010, 114, 7830-7843) using Amber with the
CHARMM36 forcefield. One concern that I have is that the barostat used in
the Klauda paper (Nose-Hoover Piston is used to maintain pressure) and the
Lenard-Jones switching function can't be implemented in Amber. Does anyone
have experience with such an endeavor? In discussions with Richard W.
Pastor, it has been clear that these parameters are particularly important
for getting bilayer properties correct.
Any help would be greatly appreciated.
--
Shalini Gupta
Visiting Undergraduate Student
University of California, San Francisco
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Received on Wed May 27 2015 - 12:30:02 PDT
