[gmx-users] Poor exchange probability for REMD

ÏéÇ« ¿× iconsdkxq at yahoo.com.cn
Fri Nov 18 02:43:11 CET 2011

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

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