[gmx-users] window exchange umbrella sampling

[Michael Shirts]

You need to have different pull parameters at the end states. Right
now, pull-kB1 is not defined in your code, so there is nothing to
interpolate to: it assume pull-kB1 = pull-k1.

Longer scale -- one would want to define reference distances that
change with lambda within the same simulation, but looking over the
code, I'm not seeing anything.  One would want to add a pull_vect1B to
change the location of the restraint as a function of lambda, but this
isn't yet defined.  That should be something we look at in the future
. . .

On Tue, Jul 16, 2013 at 2:41 PM, Parisa Akhshi <akhshi.pa at gmail.com> wrote:
> 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
> .
> .
> .
> --
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