Ah, this is a force field issue -- urey-bradley terms are not supported free energy calculations. However, since only restraints are changing, this warning doesn't really need to be there.
It would be relatively simple to put in a check to allow this to work, but it might take a week or two to get around to it. I'll file a redmine in the meantime, in case someone else can get to it first! http://redmine.gromacs.org/issues/1302 On Tue, Jul 16, 2013 at 5:32 PM, Parisa <akhshi...@gmail.com> wrote: > Thanks for quick reply. I fixed the issue with kB1. Below is what I have > changed in the .mdp file. I use this to run it "mpirun -np 3 mdrun_mpi -s > prefix_.tpr -multi 3 -replex 6 -dhdl a.dhdl". But I get this error (I am > using version 4.6.1): > > Fatal error: > Function type U-B not implemented in ip_pert > For more information and tips for troubleshooting, please check the GROMACS > > Here is the input file: > . > . > . > pull_group0 = POPC > pull_weights0 = > pull_pbcatom0 = 0 > pull_group1 = DNA > 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 > pull_kB1 = 200 > > free_energy = yes > restraint-lambdas = 1.0 0.5 0.0 > init-lambda-state = 0 > nstdhdl = 10 > . > . > . > > Any idea about it? > > Thanks, > > Parisa > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/window-exchange-umbrella-sampling-tp5009894p5009899.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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
