[gmx-users] Hamiltonian replica exchange umbrella sampling with gmx 4.6

[Michael Shirts]

Hi, Joakim-

Hamiltonian exchange only should work if there is a lambda coupling
parameter that defines the potential at each state.  You need to
define your pulling potential so that the coupling-lambda parameter
can be used to define the different pulling location centers along
your trajectory.  Does this make it clearer?


On Thu, Mar 7, 2013 at 7:26 AM, Joakim Jämbeck <jambeck at me.com> wrote:
> Dear gmx-users,
>
> I am currently trying to runt Hamiltonian replica exchange umbrella sampling in hope to do some better sampling.
>
> I have generated a number of tpr-files along my reaction coordinate and they all run fine in independent simulations. The issue comes when I would like the replica exchange to start.
>
> The following line is used to initiate the exchange:
>
> mdrun_mpi -replex 1000 -s md -pf pullf -px pullx -multi 40 -maxh 0.5
>
> All replicas have the same temperature and the following error is what I face seconds after submitting the job:
>
> The properties of the 40 systems are all the same, there is nothing to exchange
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> I could simply change the temperature between the replicas by 0.001 K and it would run I think. But that is not very elegant.
>
> Does anyone have any suggestions?
>
> Thanks in advance!
>
> Best regards,
> Joakim--
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