[gmx-users] Normal Mode Analysis

Ran Friedman r.friedman at bioc.uzh.ch
Tue Apr 27 14:08:38 CEST 2010


NMA is not MD - for one thing you don't run an NMA simulation for a
certain time. I suggest you read about NMA and make sure you understand
what the method does and what it can achieve before continuing. There is
some data on the manual, a lot of data on the web and even more in
books. When you have a good idea on what is NMA and why you're
interested in running it, you can try to run things and come back to the
list with more specific questions if such arise. In parallel, it may be
a good idea to read some papers where NMA was applied. I have in mind
papers of Lindahl and Levitt from the recent years, but you should be
able to come with an elaborate list.

Good luck,

Anirban Ghosh wrote:
> 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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