Dear Gromacs users! I have a question about umbrella sampling simulation based on the Justin's tutorial.
According to the tutorial after definition of the set of conformers extracted from the pulled trajectory I should run N equilibrating simulations and N productions runs. In the tutorial I've found that all equilibrations run in the NPT ensemble. In my case I have membrane receptor for each conformer extracted from the pulling trajectory I want to run 20 umbrella's simulations with different starting velocities in each case. Should I re-equilibrate each conformer in the nvt+npt runs (re-assigning velocities in the nvt run) or the velocities might be re-assigned in the npt equilibrations ? What the time-prolongation of each equilibrations should be for each conformer in case of membrane protein simulation? Thanks for help James -- 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
