[gmx-users] NMA problem (again and again!)

David van der Spoel spoel at xray.bmc.uu.se
Fri Feb 17 18:09:57 CET 2006

fabrizio.mancinelli at unina2.it wrote:
> Hello all,
> I've got 2 more question about normal modes analysis.
> 1) at the end of the minimization step, I got a value of about e-04 for Fmax. 
> But, when the mdrun(nm) step starts, it says that Fmax is about e+02. What 
> could have been happened?
Did you use the trr as input for the coordinates in the NM?

> 2) By the way, the hessian was built as well. During diagonalization step, the 
> program halted with the following message:
Sorry don't know, but could be that it is not minimized enough
> -------------------------------------------------------
> Program g_nmeig_d, VERSION 3.3
> Source code file: eigensolver.c, line: 223
> Fatal error:
> Unspecified error from Arnoldi diagonalization:3
> -------------------------------------------------------
> The protein was a oligomer of 438 aa in vacuum. The electrostatic treatment 
> was a shifted potential as suggested by David in an earlier post.
> Thanks, 
> Fabrizio
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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