I am aware of the tutorial and guidelines for REMD by Mark Abraham on GROMACS website. I have 48 replicas, I calculated temperatures using the REMD temperature calculator server where the exchange probability was taken as 0.25. My replica exchange is at NPT. After 10ns of run in 12 hour, I get average exchange probability of 0.12 and 0.55 for replicas 15 and 16 respectively. Do I need to adjust the temperatures or it is ok to have such probabilities in REMD?
My other question is about restarting REMD runs in GROMACS. I have 48 replicas hence 48 directories. Within each directory, I have multiple log files (md_0_1.log, md_0_2.log, etc) and trajectories (md_0_1.xtc, md_0_2.xtc, etc). How do I combine these files and also from other directories to obtain trajectory at particular temperature?
About the second question, do you want the track of for example system1 and bring all the system1 trajectories together?
Dear Neha,
I would consider best practice, in a thermodynamical spirit, to have an overall exchange probability close to 0.25. For this purpose, you can tune: a) the differences in temperature between replicas, (and/or) b) the time between replica exchanges.
- About your second question: Quoting from Gromacs documentation (http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/An_introduction_to_replica_exchange_simulations%3A_Mark_Abraham,_Session_1B)
"There are some times you want a trajectory that has continuous coordinates, despite the "jumps" in ensemble space. This means chopping up each trajectory file into pieces and pasting them back together in the right order. The Perl script demux.pl installed with GROMACS will analyse a single REMD .log file and writes two special .xvg files that describe the transformation matrices for the trajectory time series from one form to the other, and back. trjcat -demux can use these files to do the cut-and-paste on the trajectory files for you."
Happy REMD simulations! (May the replica be with you)
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