Hi, 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. Franzi 2009/5/26 Berk Hess <g...@hotmail.com> > 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 > > > > ------------------------------ > Express yourself instantly with MSN Messenger! MSN > Messenger<http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/> > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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