[gmx-users] Hamiltonian replica exchange not working in 4.6

Michael Shirts mrshirts at gmail.com
Wed Aug 7 04:55:41 CEST 2013

Hi, Sanku-

The way to invoke Hamiltonian replica exchange has changed to be a bit
more flexible.  We should go back and make sure that this legacy way
is supported (I thought this invocation was supported, but apparently
it isn't), but what you should be able to do to get it working quickly
is include in all the .mdp files the line:

fep-lambdas  0 0.08 . . . . . . 1.0

I.e. list all of the lambdas that all of the files use.  This is
described in the documentation.

It should run correctly then.  If not, then bug me on the list again.

On Tue, Aug 6, 2013 at 6:52 PM, Sanku M <msanku65 at yahoo.com> wrote:
> Dear Gromacs user,
>   I am not sure whether this is any potential bug. But I found that in gromacs4.6.3, hamiltonian replica exchange simulation is not
> working. The SAME simulation works perfectly fine in gromacs 4.5.4
> But, when I try to run the simulation using gromacs4.6.3, I get following error:
> "The properties of the 10 systems are all the same, there is nothing to exchange
> For more information and tips for troubleshooting, please check the GROMACS"
> Here is the details on the error:
>    I have first defined A and B state by scaling the relevant parameter.. Then I have  generated different tpr file by using mdp file which only differ by 'init-lambda' parameter:
> For example, I have 10 different mdp files: Free energy part of two of them are shown below:
> for hremd0.mdp, the relevant part for free energy part is
>   ; Free energy control stuff
> free_energy  = yes
> init-lambda              = 0
> delta_lambda = 0
> for hremd1.mdp
> ; Free energy control stuff
> free_energy  = yes
> init-lambda              = .080
> delta_lambda = 0
> ..
> and so on..
> The rest of mdp portions are same for all the mdp files...
> However, with gromacs4.5.4, the same simulation works without problem. I do not get the error that all the systems are identical.
> In both cases, I am using same system with OPLS forcefield..
> The way I run the simulations is:
> mpirun -np 10 mdrun_463 -multi 10 -v -s hremd -replex 250 -c &>log_repl
> Any help will be appreciated.
> Sanku
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