xi zhao wrote: > I performed remd using GROMACS 3.3.1 at four different temperatures: > 270k, 400k, 540k, 660k, and produced four trajectories. I want to know > whether my simulation is ok, but I do not know how to analysis my > trajectories.
Probably these temperatures are spaced far too widely if you are not doing a vacuum simulation of a small peptide. Check literature for more suitable temperature ranges. > Though I have demux.pl script and produced > replica_index.xvg and replica_temp.xvg files, the contents of two files > are the same! I'm not familiar with the contents of theses files, but if your temperatures are too widely spaced, you won't see exchanges, and that might be the reason for these files being identical. > I use trjcat_d to produce a continuous > trajectory,according to wiki gromacs. In fact, for a REMD > simulation, I can not judge whether the simulations is ok , and if they > are ok, how to further analyze or extract useful information from > trajectories! Are you clear? This question is common to all other MD simulations, and the answer to it depends on the purpose for the calculations. To get some ideas, have a look at the literature for similar calculations, do background reading and be prepared to think hard. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
