[gmx-users] Normal Mode Analysis

Franzi Hoffgaard f.hoffgaard at gmail.com
Tue May 26 12:40:36 CEST 2009


as I wrote in the first message, I tried renaming it with the extension .trj
and yielded segmentation faults. I also tried it with the extension .trr and
got the error message:

trn version: VERSION 4.0.4
Program gmxdump_d, VERSION 4.0.4
Source code file: trnio.c, line: 69

Fatal error:
Float size 3556. Maybe different CPU?

Both extensions didn't work.

There is just another little question that came into my mind. As I said I
performed the NMA with gromacs 3.2.1 and 4.0.x both with the same system and
setup. I would expect that the .mtx-files have similar sizes, but using
version 4.0.x the file-size is about 300 Mb and using the version 3.2.1 it
is about 7 Gb.


2009/5/26 Berk Hess <gmx3 at hotmail.com>

>  Hi,
> Try renaming it with the extension .trr iso .trj.
> Berk
> ------------------------------
> Date: Tue, 26 May 2009 10:53:32 +0200
> From: f.hoffgaard at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Normal Mode Analysis
> Hi,
> I'm quite a new user of gromacs. I want to do an all-atom normal mode
> analysis of a small protein in water. As a result I would like to have the
> hessian matrix in a readable format, that I can use for further
> computations.
> As I have read in the manuals/tutorials/mailing-lists I minimized the whole
> system (at first with the steepest descent integrator for a couple of steps
> and later on with the l-bfgs integrator to become a maximum force close to
> zero). Afterwards I created the run input file (with the nm integrator)
> using the high precision trajectory from the minimization. This and the
> following call of mdrun worked fine. As a result I became the hessian.mtx.
> As I said I want the matrix in ASCII format, so I followed the instructions
> and renamed the file into hessian.trj and ran "gmxdump_d -f mat2.trj" and
> got a Segmentation fault.Trying gmxcheck also led to Segmentation fault. I
> tried same procedure but using trr instead of trj as file-ending. Both, for
> gmxcheck and gmxdump I yielded the following message:
> trn version: VERSION 4.0.4
> -------------------------------------------------------
> Program gmxdump_d, VERSION 4.0.4
> Source code file: trnio.c, line: 69
> Fatal error:
> Float size 3556. Maybe different CPU?
> -------------------------------------------------------
> I tried "g_traj -ox" as well without any result. This led me to the
> conclusion that the file is corrupt, but I just tried diagonalizing the
> hessian matrix using "g_nmeig" anyway. Surprisingly this yielded no error
> message and I ended up with the first 50 eigenvalues and -vectors. So
> despite my first assumption the file cannot be corrupt. Or am I wrong?
> The architecture/s I worked on are:
> 1. Suse Linux 10.3, 64 bit, Intel Processor, quad-core (gromacs 4.0.3)
> 2. Mac OS X 10.5 (Leopard), Intel Proc. 2 x quad-core (gromacs 4.0.4,
> gromacs 4.0.5)
> The results were on both architectures the same. But ...
> I read in a former email of this mailing list of a similar problem and that
> the problem did not occur in the gromacs version 3.2.1. So I uninstalled
> gromacs 4.0 and installed gromacs 3.2.1 and  performed the last stage of
> minimization and the computation of the hessian matrix. This binary file
> yielded no error using gmxdump and gmxcheck. (Input files for the l-bfgs and
> nm step were not changed.)
> So, my question is, is this a bug of the newer gromacs version/s or did I
> something wrong. As I would like to stick to a newer version of gromacs, I
> am wondering, what else (than downgrading) can I do to get the hessian
> matrix in a human readable format out of the normal mode analysis.
> Best regards, Franziska
> ---
> Franziska Hoffgaard
> PhD Student
> Bioinformatics & Theo. Biology Group
> TU Darmstadt
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