[gmx-users] window exchange umbrella sampling

[Parisa Akhshi]

I am trying to use Hamiltonian replica exchange as implemented in Gromacs.
The idea is to use different pulling umbrella forces and then obtain a PMF
profile. I am specifically interested in exchanging force constants between
windows.

To do a quick test, I successfully ran replica exchange in which the
temperature is exchanged. In this case, I prepared for example 8 tpr files
at 8 different temperatures and run them using

mpirun -np 8  mdrun_mpi -s prefix_.tpr -multi 8 -replex 100

And it ran just fine.

For window exchange umbrella sampling, though, I am confused with the input
preparation. I am not sure how to specify in the .mdp file how the values
of pull force should be used to define different force constants for
different replicas. Also, when submitting the job, how should I ask the
program to exchange pull forces between windows? I tried using  this:

http://lists.gromacs.org/pipermail/gmx-users/2011-April/060448.html

But, it gives me the error:

Fatal error:
The properties of the ... systems are all the same, there is nothing to
exchange

I noticed a previous discussion on below link:

http://gromacs.5086.x6.nabble.com/Hamiltonian-replica-exchange-umbrella-sampling-with-gmx-4-6-td5006187.html

However, I am not sure how to use the restraint-lambda parameter exactly.
Is there any example, ... how to use it?

I have copied the related portion of one of the the .mdp files below for
moving MOL2 with respect to MOL1

Thanks for your help,

Parisa




.
.
.
pull_group0              = MOL1
pull_weights0            =
pull_pbcatom0            = 0
pull_group1              = MOL2
pull_weights1            =
pull_pbcatom1            = 0
pull_vec1                = 0.0 0.0 0.0
pull_init1               = 0.0 0.0 0.0
pull_rate1               = 0
pull_k1                  = 300

free_energy              = yes
restraint-lambdas  =  0.0 0.5 1.0 0.0 0.5 1.0 0.0 0.5 1.0
.
.
.