Hi,
Try renaming it with the extension .trr iso .trj.
Berk
Date: Tue, 26 May 2009 10:53:32 +0200
From: f.hoffga...@gmail.com
To: gmx-users@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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