<html>
<head>
<style><!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 10pt;
font-family:Verdana
}
--></style>
</head>
<body class='hmmessage'>
Hi Carsten<div>I checked again and the segmentation fault appears to be unrelated to file size. I obtained the</div><div>eigenvector.trr files that give a seg fault using the g_covar -nofit option as I had already fit the data</div><div>using trjconv -fit rot+trans. This would mean the reference structure file is not saved in the .trr file. Also, these eigenvector.trr files were generated using gromacs 4.07.</div><div>The eigenvector.trr files that work with make_edi were generated using gromacs 3.3 and g_covar -fit.</div><div>I can't think of any other difference between the .trr files I have.</div><div><br></div><div>In any case I am running a new g_covar with the -fit option to see if that is the problem.</div><div>Thanks</div><div>Vijaya</div><div><br></div><div><br></div><div><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>
<span class="ecxApple-style-span" style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:14px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span class="ecxApple-style-span" style="border-collapse:separate;color:rgb(0, 0, 0);font-family:Helvetica;font-size:14px;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 style="word-wrap:break-word"><div><span class="ecxApple-style-span" style="font-size:medium"><br></span></div></div></span></span></div></div></div> <br /><hr />The New Busy is not the old busy. Search, chat and e-mail from your inbox. <a href='http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_3' target='_new'>Get started.</a></body>
</html>