Re: [AMBER] How to choose between implicit and explicit solvent

From: Josh Berryman <>
Date: Mon, 9 Nov 2015 21:43:37 +0100

"I would like to get some inputs from somebody with some experience with
drugs and MD."

Big mistake. Might be OK just looking at the simulations, but don't get
high and start messing around with an expensive shared supercomputer.

Of course you could get a personal GPU in which case you are hurting noone,
5 million atoms should fit on a Tesla K40, a K80 is twice as big although
it hasn't made it onto the "supported cards" list here: . I'd be tempted to have a go at
that myself, it sounds like a fun calculation. Off-topic: a K80 looks like
it is just two K40s in a box, does anyone know if you can use it OK as a
single card?

An alternative approach to going brute force on a big GPU would be to to
measure nucleation rates via some kind of umbrella sampling or
path-sampling, or maybe hamiltonian replica exchange with respect to the
water-drug coupling strength. Doing free energy methods across a phase
transition can be a little bit problematic, to be honest if you don't have
much experience then you should probably just get a big graphics card and
go brute force.

Have a look at the free energy/thermodynamic integration section of the
manual. You will need to have a decent background in statistical mechanics
to successfully pull of a calculation of that kind for the very complicated
scenario that you outline, but it might turn out to be the only option.

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Received on Mon Nov 09 2015 - 13:00:04 PST
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