On Wed, May 27, 2015 at 3:22 PM, Shalini Gupta <gshalini21294.gmail.com>
wrote:
> 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.
>
Amber 14 supports a Monte Carlo barostat which should be as good as the
Langevin piston. Richard Pastor's concern with respect to Amber barostats
is almost certainly aimed at the Berendsen barostat, which has known
problems in terms of producing incorrect volume distributions (the
fluctuations are too small). The MC barostat does not suffer from this
problem.
As for the L-J switch, Amber has no such option. CHARMM-GUI spits out
Amber-compatible input files if you generate your bilayer that way, and
their recommended approach is to simply use a 10 to 12 A cutoff with no
switch, and it seems to do reasonably well.
HTH,
Jason
-
-
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 27 2015 - 14:00:02 PDT
