[gmx-users] pressure based replica exchange

Thu Dec 12 15:49:00 CET 2013

Hamiltonian replica exchange based around the free energy
functionality is in GROMACS, though it would be interesting to explore
the PLUMED options more to understand the differences . . .

On Thu, Dec 12, 2013 at 5:48 AM, 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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