[gmx-users] Normal Mode Analysis

Anirban Ghosh reach.anirban.ghosh at gmail.com
Tue Apr 27 08:53:13 CEST 2010


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.


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