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
--
========================================
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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