As you can see in your plot, no replicas from 400K got down to 300K in the 1.5ns you simulated. So you've so far derived no benefit from REMD (unless you want sampling at lots of temperatures). Perhaps a simulation a hundred times longer might get a few such events? You might as well have run a simulation at 400K to see what it did... What do you hope REMD will help you observe?
Mark On Fri, Mar 22, 2013 at 12:28 PM, Albert <mailmd2...@gmail.com> wrote: > Hello: > > I've finished a replica exchange simulation with 72 replica (300K-580K) > under explicit solvent model. It generate 72 trajectory and the replica > since to "cross" well with neighboring temperature. Here is the figure: > > > http://dl.dropbox.com/u/**56271062/REMD.png<http://dl.dropbox.com/u/56271062/REMD.png> > > I am just wondering how can we generate and visualize the system at 300 K > with that at 400-500 K? There is a ligand in my system, and it is expected > to escape binding pocket with large loop movement.... > > thank you very much > > best > Albert > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
