[gmx-users] pressure based replica exchange

[Mark Abraham]

Quite right, sorry. P as the control variable is not implemented. NPT with
T as the control variable is, for example.

Mark


On Thu, Dec 12, 2013 at 5:58 PM, Michael Shirts <mrshirts at gmail.com> wrote:

> Pressure replica exchange is not in currently. It will be added
> eventually (it's not that hard, just takes time, and hasn't been a
> priority.).
>
> Note that pressure temperature control with berendsen pressure control
> will be 100% wrong.  For pressure replica exchange to work, the
> barostat has to give the correct volume fluctuations, and berendsen
> does not give correct volume fluctuations.
>
> Of course, that's irrelevant since pressure replica exchange isn't in yet.
>
> The exchange criteria is always of the form min(1,exp(-X), where X =
> \beta(Delta (beta U) + Delta (beta P V)).  Where P, beta, and U can
> vary with state.
>
> What is in is temperature replica exchange with NPT, where beta
> changes, but P stays the same.
>
> On Thu, Dec 12, 2013 at 1:40 AM, Jianguo Li <ljggmx at yahoo.com.sg> wrote:
> > Thanks very much. As you suggested, making T with small increments such
> as 300.0, 300.0001, 300.0002 ... leads to complaints :-)
> >
> > I am trying to do replica exchange at different surface tensions for my
> membrane system.
> > To achieve different surface tensions for different replica, I only
> changed Pxy, but keep Pz the same for all replica.
> > pcoupl          = berendsen
> > pcoupltype      = semi-isotropic
> > tau_p           = 0.5 0.5
> > ref_p           = 1.0 1.0  ; Pxy and Pz
> > compressibility = 4.5e-5  4.5e-5
> >
> > I noticed that in the manual, the eq (3.141) shows the exchange
> probability. Can you explain what does the P1 and P2 represent? Pxy or Pz?
> >
> > Also, the manual mentioned about using Hamiltonian and temperature
> replica exchange simultaneously (eq 3.143). But there is no pressure term
> in the acceptance criteria (eq 3.143). I am wondering if
> pressure+temperature+Hamiltonian replica exchange has been implemented in
> Gromacs. If yes, what is the general equation of acceptance criteria?
> >
> > Cheers,
> > Jianguo
> >
> >
> >
> >
> >
> >
> >
> > On Tuesday, 10 December 2013, 17:49, Mark Abraham <
> mark.j.abraham at gmail.com> wrote:
> >
> >
> >
> >
> >
> >
> > On Tue, Dec 10, 2013 at 1:47 PM, Jianguo Li <ljggmx at yahoo.com.sg> wrote:
> >
> > Dear All,
> >>
> >>Is it possible to do pressure based replica exchange simulations in
> gromacs? Basically I want to do replica exchange simulations for my
> membrane system at different surface tensions. If I just set different
> pressures in the mpd file, then the mdrun will complain "systems are all
> the same, there is nothing to exchange". Is there any other parameters I
> need to set?
> >>
> >
> > Yes, the implementation is a bit broken, and requires that one of ref-t
> or lambda varies before it even considers the pressure. If you want T
> constant and P as the replica control variable, you can can only do that by
> fooling the implementation by having T vary in tiny increments.
> >
> > Mark
> >
> >
> >>Thanks a lot!
> >>
> >>Jianguo
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