Hi,<br><br>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:<br><br>trn version: VERSION 4.0.4<br>
-------------------------------------------------------<br><div class="h5">Program gmxdump_d, VERSION 4.0.4<br>Source code file: trnio.c, line: 69<br><br>Fatal error:<br>Float size 3556. Maybe different CPU?<br>
-------------------------------------------------------<br><br>Both extensions didn't work. <br><br><br>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.<br>
<br>Franzi <br></div><br><br><br><div class="gmail_quote">2009/5/26 Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com">gmx3@hotmail.com</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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Hi,<br><br>Try renaming it with the extension .trr iso .trj.<br><br>Berk<br><br><hr>Date: Tue, 26 May 2009 10:53:32 +0200<br>From: <a href="mailto:f.hoffgaard@gmail.com" target="_blank">f.hoffgaard@gmail.com</a><br>To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] Normal Mode Analysis<div><div></div><div class="h5"><br><br>Hi,<br><br>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.<br>
<br>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.<br>
<br>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:<br>
<br>trn version: VERSION 4.0.4<br>-------------------------------------------------------<br>Program gmxdump_d, VERSION 4.0.4<br>Source code file: trnio.c, line: 69<br><br>Fatal error:<br>Float size 3556. Maybe different CPU?<br>
-------------------------------------------------------<br><br>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?<br>
<br>The architecture/s I worked on are:<br>1. Suse Linux 10.3, 64 bit, Intel Processor, quad-core (gromacs 4.0.3)<br>2. Mac OS X 10.5 (Leopard), Intel Proc. 2 x quad-core (gromacs 4.0.4, gromacs 4.0.5)<br><br>The results were on both architectures the same. But ...<br>
<br>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.)<br>
<br>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.<br>
<br>Best regards, Franziska<br><br>---<br>Franziska Hoffgaard<br>PhD Student<br>Bioinformatics & Theo. Biology Group<br>TU Darmstadt<br><br><br><br></div></div><div class="hm"><hr>Express yourself instantly with MSN Messenger! <a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/" target="_blank">MSN Messenger</a></div>
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