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.
4. Anyway, sander and pmemd alone (without plumed)* I think* support
Hamiltonian replica exchange (I know people using it).
Regards,
Giovanni
On Wed, Dec 14, 2016 at 11:48 PM, Neale, Christopher Andrew <cneale.lanl.gov
> wrote:
> I'm available to test and debug from a user's perspective if anybody is
> interested in implementing it. It's possible to do with the plumed plugin,
> but that's only compatible with Amber14 at the moment and I need the
> force-based switching that is available in Amber16.
>
> In the past, I have helped to test the pressure-coupling aspect of the
> plumed code (as a plugin to gromacs). The energy contribution is actually
> almost vanishingly small, and although ideally one would consider it
> explicitly I'd be happy for the moment to simply be able to do NPT T-REMD
> in amber16 without taking this term into account so if it's just a matter
> of commenting out some line of code that disallows NPT T-REMD given that
> the pressure/volume component is not accounted for then I'd appreciate it
> if somebody could give me a hint as to where to look in the code to do this.
>
> Thank you,
> Chris.
>
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> From: Adrian Roitberg <roitberg.ufl.edu>
> Date: Tue, 13 Dec 2016 09:23:39 -0500
>
> Hi
>
> Not that I know.
>
> The changes should not be very hard to do, but testing and debugging
> might be hard, since no one within the amber developers is really
> working on T-REMD with constant pressure.
>
> adrian
>
>
>
> On 12/12/16 3:44 PM, Neale, Christopher Andrew wrote:
> > Dear Users:
> >
> > Does anybody have a modified version of amber16 that can do temperature
> replica exchange with pressure coupling? I'd like to do T-REMD with lipid
> bilayer systems, but it seems to be impossible at present.
> >
> > Here's the error message that I get:
> >
> > | ERROR: REMD cannot be run with ntp > 0!
> >
> > When I try to run with options like this:
> >
> > ! Constant pressure control. Note that ntp=3 requires barostat=1
> > barostat=2,
> > ntp=3,
> > pres0=1.01325,
> > taup=4,
> > comp=45,
> > csurften=3,
> > gamma_ten=0.0,
> > ninterface=2,
> >
> >
> > Thank you,
> > Chris.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Dec 15 2016 - 00:30:02 PST
