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

David van der Spoel spoel at xray.bmc.uu.se
Mon Feb 20 15:02:13 CET 2006

Fabrizio Mancinelli wrote:
> 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?
nm computes forces, and no program read or writes forces to a tpr file, 
although the format supports it.

> 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://folding.bmc.uu.se

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