[gmx-users] pressure based replica exchange
ljggmx at yahoo.com.sg
Thu Dec 12 07:41:11 CET 2013
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?
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:
>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.
>Thanks a lot!
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