I am new to membrane dynamics simulation. In recent days i learnt to build a membrane dynamics system, but i doubt whether my system is properly made or not. I checked results of energy minimization, NVT, NPT and solvation layer too, everything is fine. But when i am performing a protein of 300 residues in lysozyme in water, the efficiency of my workstation is it can run 7.5 ns per day. For the same protein, when i am making the membrane simulation system, the efficiency of my workstation becomes it can complete 12 ns per day. Is this a common thing or a strange situation, where i might have commited some mistakes in preparing the system. Hoping for good suggestions and thanks in advance.
Hi Kamalesh,
First of all, the efficiency of the MD simulation is not a good indicator to check. You should look for the literature regarding your system and try to reproduce some property. The speed of simulation may depend on the number of particles in your system, cut-off for interactions, neighbour list generation etc.
Thanks
Gourav Shrivastav
Ya thank you so much, now i understood the reason for longer time and things i should consider for my simulation.
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