Dear GMX users，
Recently i am performing the REMD simulation with Gromacs program and the
temperature distribution for each replica was predicted with the server
"http://folding.bmc.uu.se/remd/";. However, after a 2-ns short test simulation
with 64 replicas , i checked the exchange probability for the neighboring
replicas and find the exchange probability was about 0.3 to 0.4 (as the file i
attached )but the desired probability was 0.2. Meanwhile, i found the exchange
probabilities fluctuated markedly for each pair of replicas while ideally we
may hope they were consistent with each other. I don't know whether this is
acceptable or must be fixed up, or a longer simulation time and
pre-equilibrium at different replica temperature for each replica was needed.
The system i simulated includes 60074 atoms which consists of 155
residues,19173 waters and 14 chloridions. I first equilibrium the system for
2ns with NPT ensemble at 300K, then start the REMD simulation for 64 different
replicas (temperature ranges from 300 to 386K) with NVT ensemble and the
exchange attempt time was 2-ps(1000 integral steps).
Now i was totally puzzled and don't know how to figure out these problems,i
am eager for the help from you and any suggestions will be greatly appreciated!
Best regards!
Xiangqian Kong
--
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
