Hi ALL, This may sound like a very basic question, but I am still pondering over it. I have simulated a membrane protein system for 30 ns after Steepest Descent minimization and now I want to perform NMA. From the help pages what I understand is that I need a very well minimized system (using l-bfgs) and then generate a Hessian matrix. My question is that after my 30 ns run, should I again go for another run of minimization with l-bfgs and the should I run MD using "nm" as the integrator? For how long should I run this MD with "nm" integrator? Is a 1 ns run enough? Or am I required to run it for 30 ns (for which I have run the normal MD)? Any suggestion is welcome. Thanks a lot in advance.
Regards, Anirban
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