[gmx-users] Poor exchange probability for REMD
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Nov 18 17:14:20 CET 2011
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
More information about the gromacs.org_gmx-users
mailing list