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Hi<br>I checked again with Gromacs 4.0.7 and I find that I have a problem<br>with make_edi when I use eigenvec.trr files generated using g_covar<br>-nofit. I use the -nofit option because the data was already fit to a reference structure<br>using trjconv -fit rot+trans.<br>I end up with a segmentation fault when I use the following command:<br><br>make_edi -linfix "4,5,7,8" -outfrq 500 -f evec170nfit.trr -s fframe170compact.gro -o edsamp.edi -linstep ".000001 .000001 .000001 .000001"<br><br>As before I get the following message:<br><br> :-) G R O M A C S (-:<br><br> Good ROcking Metal Altar for Chronical Sinners<br><br> :-) VERSION 4.0.7 (-:<br><br><br> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.<br> Copyright (c) 1991-2000, University of Groningen, The Netherlands.<br> Copyright (c) 2001-2008, The GROMACS development team,<br> check out http://www.gromacs.org for more information.<br><br> This program is free software; you can redistribute it and/or<br> modify it under the terms of the GNU General Public License<br> as published by the Free Software Foundation; either version 2<br> of the License, or (at your option) any later version.<br><br> :-) make_edi (-:<br><br>Option Filename Type Description<br>------------------------------------------------------------<br> -f evec170nfit.trr Input Full precision trajectory: trr trj cpt<br>-eig eigenval.xvg Input, Opt. xvgr/xmgr file<br> -s fframe170compact.gro Input Structure+mass(db): tpr tpb tpa gro<br> g96 pdb<br> -n index.ndx Input, Opt. Index file<br>-tar target.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br>-ori origin.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa<br> -o edsamp.edi Output ED sampling input<br><br>Option Type Value Description<br>------------------------------------------------------<br>-[no]h bool no Print help info and quit<br>-nice int 0 Set the nicelevel<br>-[no]xvgr bool yes Add specific codes (legends etc.) in the output<br> xvg files for the xmgrace program<br>-mon string Indices of eigenvectors for projections of x<br> (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91<br>-linfix string 4,5,7,8 Indices of eigenvectors for fixed increment<br> linear sampling<br>-linacc string Indices of eigenvectors for acceptance linear<br> sampling<br>-flood string Indices of eigenvectors for flooding<br>-radfix string Indices of eigenvectors for fixed increment<br> radius expansion<br>-radacc string Indices of eigenvectors for acceptance radius<br> expansion<br>-radcon string Indices of eigenvectors for acceptance radius<br> contraction<br>-outfrq int 500 Freqency (in steps) of writing output in .edo file<br>-slope real 0 Minimal slope in acceptance radius expansion<br>-maxedsteps int 0 Max nr of steps per cycle<br>-deltaF0 real 150 Target destabilization energy - used for flooding<br>-deltaF real 0 Start deltaF with this parameter - default 0,<br> i.e. nonzero values only needed for restart<br>-tau real 0.1 Coupling constant for adaption of flooding<br> strength according to deltaF0, 0 = infinity i.e.<br> constant flooding strength<br>-eqsteps int 0 Number of steps to run without any perturbations <br>-Eflnull real 0 This is the starting value of the flooding<br> strength. The flooding strength is updated<br> according to the adaptive flooding scheme. To use<br> a constant flooding strength use -tau 0. <br>-T real 300 T is temperature, the value is needed if you want<br> to do flooding <br>-alpha real 1 Scale width of gaussian flooding potential with<br> alpha^2 <br>-linstep string .000001 .000001 .000001 .000001 Stepsizes (nm/step) for<br> fixed increment linear sampling (put in quotes!<br> "1.0 2.3 5.1 -3.1")<br>-accdir string Directions for acceptance linear sampling - only<br> sign counts! (put in quotes! "-1 +1 -1.1")<br>-radstep real 0 Stepsize (nm/step) for fixed increment radius<br> expansion<br>-[no]restrain bool no Use the flooding potential with inverted sign -><br> effects as quasiharmonic restraining potential<br>-[no]hessian bool no The eigenvectors and eigenvalues are from a<br> Hessian matrix<br>-[no]harmonic bool no The eigenvalues are interpreted as spring constant<br><br>list -linfix consist of the indices:4 5 7 8 <br>list -linacc consist of the indices:<br>list -flood consist of the indices:<br>list -radfix consist of the indices:<br>list -radacc consist of the indices:<br>list -radcon consist of the indices:<br>list -mon consist of the indices:<br>trn version: GMX_trn_file (single precision)<br>Eigenvectors in evec170nfit.trr were determined without fitting<br>Read non mass weighted average/minimum structure with 4128 atoms from evec170nfit.trr<br>Read 2000 eigenvectors (for 4128 atoms)<br><br><br>Select an index group of 4128 elements that corresponds to the eigenvectors<br>Opening library file /sw/analysis/gromacs/4.0.7/centos5.4_pgi8.0.4/share/gromacs/top/aminoacids.dat<br>Group 0 ( System) has 4128 elements<br>Group 1 ( Protein) has 4128 elements<br>Group 2 ( Protein-H) has 4128 elements<br>Group 3 ( C-alpha) has 4128 elements<br>Group 4 ( Backbone) has 4128 elements<br>Group 5 ( MainChain) has 4128 elements<br>Group 6 (MainChain+Cb) has 4128 elements<br>Group 7 ( MainChain+H) has 4128 elements<br>Group 8 ( SideChain) has 0 elements<br>Group 9 ( SideChain-H) has 0 elements<br>Select a group: 3<br>Selected 3: 'C-alpha'<br><br>Segmentation fault<br><br>With the eigenvector.trr generated using g_covar -fit option I don't get the <br>segmentation fault. The following line in the above log file <br>" Eigenvectors in evec170nfit.trr were determined without fitting" is replaced instead<br>with <br>"Read non mass weighted reference structure with 4128 atoms from evec170fit.trr"<br>and I get the edsamp.edi file.<br><br>I already performed covariance analyses using the -nofit option on my large protein and would like to use the results I have so far if possible. If anyone knows <br>what the problem is, it would be of great help.<br><br>Thanks <br>Vijaya<br><br><hr id="stopSpelling">From: ckutzne@gwdg.de<br>Subject: Re: [gmx-users] make_edi<br>Date: Fri, 23 Apr 2010 10:05:12 +0200<br>To: gmx-users@gromacs.org<br><br>
Hi <span class="ecxApple-style-span" style="font-family: Verdana; font-size: 13px;">Vijaya,</span><div><font class="ecxApple-style-span" face="Verdana" size="3"><span class="ecxApple-style-span" style="font-size: 13px;"><br></span></font></div><div><font class="ecxApple-style-span" face="Verdana" size="3"><span class="ecxApple-style-span" style="font-size: 13px;">what version of Gromacs is this and how big do the trr files</span></font></div><div><font class="ecxApple-style-span" face="Verdana" size="3"><span class="ecxApple-style-span" style="font-size: 13px;">have to be so that the segv shows up?</span></font></div><div><font class="ecxApple-style-span" face="Verdana" size="3"><span class="ecxApple-style-span" style="font-size: 13px;"><br></span></font></div><div><font class="ecxApple-style-span" face="Verdana" size="3"><span class="ecxApple-style-span" style="font-size: 13px;">Carsten</span></font></div><div><font class="ecxApple-style-span" face="Verdana" size="3"><span class="ecxApple-style-span" style="font-size: 13px;"><br></span></font></div><div><font class="ecxApple-style-span" face="Verdana" size="3"><span class="ecxApple-style-span" style="font-size: 13px;"><br></span></font></div><div><font class="ecxApple-style-span" face="Verdana" size="3"><span class="ecxApple-style-span" style="font-size: 13px;"><br></span></font><div><div>On Apr 22, 2010, at 6:56 PM, vijaya subramanian wrote:</div><br class="ecxApple-interchange-newline"><blockquote><span class="ecxApple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;"><div class="ecxhmmessage" style="font-size: 10pt; font-family: Verdana;">Hi<br>When I run make_edi with a small eigenvec.trr file it works, but gives me a segmentation fault when I input large .trr files generated using g_covar. These large eigenvector<br>files work well with g_anaeig and I have used them to generate projections as well as filtered trajectories.<br>The command line with options for make_edi is given below:<span class="ecxApple-converted-space"> </span><br><br>make_edi -linfix "4,5,7,8" -outfrq 500 -f eigvec.trr -s fframe.gro -o edsamp.edi -linstep ".0001 .0001 .0001 .0001"<br><br><br>One option would be to read the large eigenvec.trr file and write out only the eigenvectors<br>I need to a new file. Is there some way I can do that? Else, is there some way to modify<br>make_edi so I don't get a segmentation fault.<br><br>Thanks<br>Vijaya<br><br><hr>The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail.<span class="ecxApple-converted-space"> </span><a href="http://www.windowslive.com/campaign/thenewbusy?tile=multicalendar&ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_5">Get busy.</a><span class="ecxApple-converted-space"> </span>--<span class="ecxApple-converted-space"> </span><br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="ecxApple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="ecxApple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="ecxApple-converted-space"> </span><br>www interface or send it to<span class="ecxApple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="ecxApple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></span></blockquote></div><br><div>
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