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

[Fabrizio Mancinelli]

If you mean "-t traj.trr" option of grompp, where traj.trr is the minimization 
trajectory (provided switched on forces writing), yes I did.
I also gmxdump'd the traj.trr file to check whether the forces are actually 
there, and they were.
After grompping (with -t option) , I gmxdump'd the resulting topol.tpr file, 
and there were coordinates, velocities, but where it is supposed the forces 
should be, appeared instead:

not available: f

Then I got crazy and I'm still wondering what won't work.
By the way, does the nm routine calculates forces from the coordinates or 
takes what I provide with -t option?

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.
________________________________________________________________________
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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