[gmx-users] NMA proctocol
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
> 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users