Re: [AMBER] Dear AMBER members,

From: David Case <>
Date: Sun, 9 Dec 2018 13:39:56 +0000

On Sun, Dec 09, 2018, 임호철(대학원/일반대학원 생명과학부(생명공학)) wrote:
>I bought Amber18 as an academic user for FEP on GPU,
>but failed to find any tutorials about 'FEP' (maybe pmemd).

Amber is moderately heavily tilted towards Thermodynamic Integration
(TI) as a means for carrying out free energy calculations for alchemical
transformations. An alternative, FEP-like, method is BAR or MBAR, which
is discussed in the Reference Manual, but not so much (as far as I can
see) in the tutorials. Still, both MBAR and TI require simulations at
multiple (fixed) lambda values, and differ only post-processing. So
following the "Thermodynamic integration using soft-core potentials"
tutorial would get you a long way along the FEP route.

....good luck....dac

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Received on Sun Dec 09 2018 - 06:00:05 PST
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