Most often, people only analyze conformations drawn from the target temperature (e.g. room temperature). There are reasons to look at higher temperatures (e.g. to decompose entropy/enthalpy or if your system has biologically or chemically relevant temperature-dependence) but you can probably ignore that for your initial analysis.
You should not eliminate any conformations drawn immediately after an exchange. The whole point of REMD is that all of your conformations are in thermal equilibrium, even those right after an exchange. However, you should do some block averaging and consider discarding some of the data obtained from the initial portion of you REMD simulation (just as you would for a standard simulation). Chris. -- original message -- I’m trying to run a REMD simulation on a protein. After a lot of reading, I am still unclear on the result analysis. Is it correct that, of many replicas, I should select the frames from only the replica with my desired temperature?(ex, room temp.) If not correct, how do I select the frames from a REMD simulation as my final structures? If correct, should I ignore some frames right after an exchange has occurred? I think they would not have reached equilibrium and therefore not to be used. I am quite confused. Any replies would be of great help. Many thanks in advance, -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
