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