[gmx-users] NMA proctocol

Justin Lemkul jalemkul at vt.edu
Sat Nov 17 01:29:48 CET 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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