[gmx-users] pressure based replica exchange

[Jianguo Li]

Thanks for the paper, I will look at it!

Cheers
Jianguo




On Thursday, 12 December 2013, 18:54, Thomas Evangelidis <tevang3 at gmail.com> wrote:
 
I'm not sure if pressure-based REMD is possible, but PLUMED-2.0 provides a
quite flexible implementation of Hamiltonian REMD for GROMACS. It may be
worth-checking it:

http://arxiv.org/abs/1307.5144




On 12 December 2013 12:11, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> 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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-- 

======================================================================

Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/

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