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 wrote:
> I'm not sure if pressure-based REMD is possible
Thanks for the paper, I will look at it!
Cheers
Jianguo
On Thursday, 12 December 2013, 18:54, Thomas Evangelidis
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:
ht
Thanks Michael and Mark.
Implementation of the pressure based replica exchange will be useful for
membrane systems as membranes will be unstable using temperature based replica
exchange.
Btw, I noticed there is a recent paper on surface tension replica exchange
simulations of membranes:
http:
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 wrote:
> Quite right, sorry. P as the control variable
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 wrote:
> Pressure replica exchange is not in currently. It will be added
> eventually (it's not that hard, just takes time,
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
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
P
On Tue, Dec 10, 2013 at 1:47 PM, Jianguo Li 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
Hi there,
In theory you may use any parameter in the Hamiltonian, but I'm pretty sure
Gromacs' REMD applies parallel tempering for temperature only. I never
looked at the actual code, but I wouldn't be surprised if it didn't even
check for differences in pressure between replicas and that's why it
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 s
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