Hello all, I am trying to understand the force vs time plots using Gromacs' umbrella sampling method. I am trying to pull a short polymer chain from the interior of a micelle and see what the PMF looks like. I use the following parameters to run the pulling simulation for 500ps to pull the polymer over a distance of 5nm:
pull=umbrella pull_geometry=direction pull_vec1=1 0 0 pull_start=yes pull_ngroups=1 pull_group0=surf pull_group1=poly pull_rate1=0.01 pull_k1=1000 After the simulation, pullf.xvg plot I obtained is a linearly increasing plot with time and similar result when pull_rate1=0.001 nm per ps. I am not sure if this is right. My question is, on what basis do we select the optimum pull_rate1 and pull_k1 for a particular system? Or is it just a choice of parameters as long as the system does not deform? How does an ideal force-time plot look like and does the choice of pull_k1 affect the histogram? It appears, the entire procedure depends on the choice of input of these two variables. I would greatly appreciate if someone can explain this concept. Thanks a lot. Andy -- View this message in context: http://gromacs.5086.x6.nabble.com/Umbrella-sampling-force-vs-time-plots-tp5009709.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
