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...@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 > . > . > . > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists