[gmx-users] Questions regarding REMD simulation

[SebastianWaltz]

Hi,
in the GROMACS implementation of REM the trajectories are exchanged not
the temperatures. The temperatures are kept constant. As well as the
description of the Okamoto paper cited by GROMACS

Basti
 

On 09/18/2011 01:35 PM, michael zhenin wrote:
> Hi All,
>
> I have few questions regarding REMD simulation.
>
> I assume REMD works in the following way: Each replica starts with a given
> temperature and the temperature of each replica changes along the simulation
> (as described in Sugita and Okamoto publication, 1999). Then demux.pl and
> trjcat collect the trajectories of the lowest temperature from each replica.
>
>
>
> My problem is that while analyzing the results, I found in the edr
> files that the temperatures along each replica are relatively
>
> constant (+- 2K from the starting temperature) and the average temperature
> is equal to the initial temperature.
>
>
> How can this be explained? Does the temperature of each replica change
> along the simulation or maybe the temperature of each
>
> simulation stays close to its initial value and the coordinates are changed
> between the different replica? (if so, why do i need to use
>
> the post-processing tools such as the demux.pl script?)
>
>
> Thanks,
>
>
> Michael
>