[gmx-users] NMA proctocol

[Justin Lemkul]

On 11/16/12 6:44 PM, Yao Yao wrote:
> Hi Gmxers,
>
>
> For Normal Mode Analysis (NMA), even I did run several rounds to aim for machine precision, with smaller emtol stepwise,
> it still did not converge to 0.001 and the Fmax is about 0.5 or so. It is just lysozyme in 200 water molecules.
>

Are you using double precision?  In any case, it may not be possible to reach 
such a low Fmax.  I'm no NMA expert, but generally isn't an Fmax < 1 or so 
considered acceptable?

> I wonder if there is a systematic way to guarantee the convergence, or I have to await luck to come.
> Because I am pretty sure if I continue with NMA, I will get translational and rotational modes in final eigenfrequencies.
>

Again, no expert on NMA, but I doubt you ever prevent the emergence of global 
translation and rotation, but you simply neglect the first 6 eigenvectors (as is 
stated in g_nmtraj, for instance).

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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