On 18/11/2011 12:43 PM, ÏéÇ« ¿× wrote:
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.
Pre-equilibration at the right temperature is always a good idea, not
just for REMD. However for NVT REMD you need to equilibrate the other
temperatures at the same box size that is sound for the temperature at
which you want to make observations.
Even given that, there is no strong reason to suppose that a temperature
distribution following a simple mathematical formula should lead to
equal exchange probabilities on a "real" system with free energy
bottlenecks. Knowing that one might need to be adding more replicas at
relevant temperatures is something that can only be determined
empirically - and probably from more than 2ns.
Mark
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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