On Thu, Dec 15, 2016 at 3:07 AM, Giovanni Bussi <giovanni.bussi.gmail.com>
wrote:
> Hi Chris,
>
> a few clarifications from the plumed side, which might be useful for other
> people reading this list:
>
> 1. Plumed is compatible with amber16. We only have patches up to amber14
> because starting with amber15 the support for plumed is included directly
> in amber.
> 2. Plumed only works with sander, and not with pmemd.
> 3. Support for Hamiltonian replica exchange shipped with plumed is only for
> gromacs. Actually, the changes required for this to work are in gromacs,
> and not in plumed. So, even with sander+plumed, you cannot use Hamiltonian
> replica exchange with sander+plumed. Even worst: sander+plumed does not
> support any form of replica exchange.
>
Are you sure about this? The way Hamiltonian REMD is implemented, the
coordinates are communicated between replicas, not the colvars. This makes
replica exchange attempts more expensive (since you have to compute the
whole potential energy instead of just the colvar), but that also makes it
much more flexible (i.e., H-REMD will typically work without having to
write code for different kinds of Hamiltonian modifications).
I *believe* H-REMD with sander + plumed will work, but that should be
validated first.
> 4. Anyway, sander and pmemd alone (without plumed)* I think* support
> Hamiltonian replica exchange (I know people using it).
>
Yes, sander, pmemd, and pmemd.cuda all support H-REMD (but only at
constant volume).
HTH,
Jason
--
Jason M. Swails
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Received on Thu Dec 15 2016 - 19:00:02 PST
