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Hi Carsten,<br>I downloaded the clone and patches, copied make_edi.c to /src/tools and<br>recompiled gromacs-4.0.7 as suggested by Mark. Now make_edi works with<br>.trr files generated using either g_covar -nofit or -fit but the .edi files generated<br>now have only the average structure recorded under both xref and xav.<br><br>For example:#NREF, XREF <br> 172 <br>1 0.989554 -2.893834 0.667306<br>2 0.825675 -2.659700 0.913271<br>3 0.760027 -2.801672 1.259611<br>4 0.500538 -2.530900 1.332710<br>5 0.292291 -2.620316 1.021137<br>6 -0.021384 -2.793121 1.143848<br>7 -0.302607 -2.782386 0.888191<br>8 -0.190402 -2.495389 0.666387<br>9 -0.237132 -2.500305 0.290461<br>.....<br>#NAV, XAV <br> 172 <br>1 0.989554 -2.893834 0.667306<br>2 0.825675 -2.659700 0.913271<br>3 0.760027 -2.801672 1.259611<br>4 0.500538 -2.530900 1.332710<br>5 0.292291 -2.620316 1.021137<br>6 -0.021384 -2.793121 1.143848<br>7 -0.302607 -2.782386 0.888191<br>8 -0.190402 -2.495389 0.666387<br>9 -0.237132 -2.500305 0.290461<br>.....<br><br>If I am not mistaken, the reference structure is needed for the ED sampling. This could be obtained from<br>the structure file <br>make_edi -s ref.gro<br><br>Thanks for your help.<br>Vijaya<br><br><br><hr id="stopSpelling">From: ckutzne@gwdg.de<br>Subject: Re: [gmx-users] make_edi, g_covar -nofit<br>Date: Wed, 5 May 2010 17:10:03 +0200<br>To: gmx-users@gromacs.org<br><br>
Hi,<div><br><div><div>On May 5, 2010, at 5:01 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>No, the original<span class="ecxApple-converted-space"> </span><span class="ecxecxApple-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;">gromacs-4.0.7 installation was not a clone from the repository. <span class="ecxApple-converted-space"> </span><br>So I uninstall that, and install the clone after getting the patches?<br></span></div></span></blockquote>This would be convenient since for more bug fixes you would then just need to</div><div>do a 'git pull' and a recompile. </div><div>Alternatively, you can, as Mark suggested, copy the make_edi.c program from the</div><div>git gromacs directory to the corresponding location in your 4.0.7 directory and</div><div>then issue a 'make' and 'make install' again.</div><div><br></div><div>Carsten</div><div><br><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;"><span class="ecxecxApple-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;">Thanks<br>Vijaya<br><br></span><br><hr id="ecxstopSpelling">From:<span class="ecxApple-converted-space"> </span><a href="mailto:ckutzne@gwdg.de">ckutzne@gwdg.de</a><br>Subject: Re: [gmx-users] make_edi, g_covar -nofit<br>Date: Wed, 5 May 2010 09:49:22 +0200<br>To:<span class="ecxApple-converted-space"> </span><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><br><div><div>On May 4, 2010, at 10:56 PM, vijaya subramanian wrote:</div><br class="ecxecxApple-interchange-newline"><blockquote><span class="ecxecxApple-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="ecxecxhmmessage" style="font-size: 10pt; font-family: Verdana;">Hi Carsten<span class="ecxecxApple-converted-space"> </span><br>A couple of quick questions:<br>I already have gromacs-4.0.7 downloaded from the gromacs website. I found that I couldn't<span class="ecxecxApple-converted-space"> </span><br>use git checkout --track -b release-4-0-patches origin/release-4-0-patches to get the patches.<br>fatal: Not a git repository<br>Do I have to uninstall gromacs-4.0.7 and re-install gromacs obtained from the git site as below,<br>then install gromacs again?<br><br></div></span></blockquote>Hi,</div><div><br></div><div>if the git clone command worked, then the git checkout --track should also work.</div><div>Maybe you forgot to change into the gromacs directory that was produced by the</div><div>first command? You have to do the checkout --track in the directory where a</div><div>.git subdir is present.</div><div><br><blockquote><span class="ecxecxApple-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="ecxecxhmmessage" style="font-size: 10pt; font-family: Verdana;">git clone<span class="ecxecxApple-converted-space"> </span><a>git://git.gromacs.org/gromacs.git</a><br></div></span></blockquote>cd gromacs<br><blockquote><span class="ecxecxApple-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="ecxecxhmmessage" style="font-size: 10pt; font-family: Verdana;">git checkout --track -b release-4-0-patches origin/release-4-0-patches<br></div></span></blockquote></div><div><br></div>Carsten<div><br><div><span class="ecxecxApple-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;"><span class="ecxecxApple-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><div><br class="ecxecxApple-interchange-newline">--</div><div>Dr. Carsten Kutzner</div><div>Max Planck Institute for Biophysical Chemistry</div><div>Theoretical and Computational Biophysics</div><div>Am Fassberg 11, 37077 Goettingen, Germany</div><div>Tel. +49-551-2012313, Fax: +49-551-2012302</div><div><a href="http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne">http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne</a></div><div><br></div></div><br class="ecxecxApple-interchange-newline"></span><br class="ecxecxApple-interchange-newline"></span></div><br></div><br><hr>Hotmail is redefining busy with tools for the New Busy. Get more from your inbox.<span class="ecxApple-converted-space"> </span><a href="http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2">See how.</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-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=""><div><br class="ecxApple-interchange-newline">--</div><div>Dr. Carsten Kutzner</div><div>Max Planck Institute for Biophysical Chemistry</div><div>Theoretical and Computational Biophysics</div><div>Am Fassberg 11, 37077 Goettingen, Germany</div><div>Tel. +49-551-2012313, Fax: +49-551-2012302</div><div><a href="http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne">http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne</a></div><div><br></div></div><br class="ecxApple-interchange-newline"></span><br class="ecxApple-interchange-newline"></span>
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