Hi, I am recently trying to perform an umbrella sampling simulation along a particular reaction coordinate on a system where I have also put position restraint on certain atoms of the system... So, for each umbrella sampling window, I have an extra potential on certain atoms ( due to the position restraint ) apart from the umbrella potential. I am using Gromacs4.5.4 for the simulation.
So, after carrying out the umbrella sampling simulation, if I use WHAM to remove the bias, I think WHAM, in its present implementation, can only remove the bias due to the umbrella potential. But the bias required for position-restraining certain atoms remains still there in the computed PMF. So, I was wondering whether you can suggest any way-out for removing that bias from the PMF due to position restraints as well. Sanku -- 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
