<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Vijaya,<div><br></div><div>could it be that you mixed something up when making the .edi file? </div><div>The tool make_edi reads the total number of atoms from the provided</div><div>.tpr file and saves this number with the other ED sampling </div><div>information to the .edi file. </div><div><br></div><div>The ED sampling module in mdrun then compares the number of atoms </div><div>from the .edi file with the .tpr file provided to mdrun - to ensure that the </div><div>.edi file was produced for the same MD system.</div><div><br></div><div>Carsten</div><div><br></div><div><br><div><div>On Jun 29, 2010, at 6:57 PM, vijaya subramanian wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">Hi<br>I need some information about how ED sampling works when<span class="Apple-converted-space"> </span><br>a subset of the atoms are used for covariance analysis. Basically I would like to<br>move the system along the first eigenvector obtained from covariance analysis of the<br>C-alpha atoms only. From the paper "Toward an Exhaustive Sampling of the Configurational Spaces of two forms of the Peptide Hormone Guanylin" it appears only the C-alpha atoms are used to define<br>the essential subspace but when I use the following commands, I get an error message saying:<br><br><br>Fatal error:<br>Nr of atoms in edsamp26-180fit.edi (4128) does not match nr of md atoms (294206)<br><font class="Apple-style-span" color="#000000" face="Helvetica"><span class="Apple-style-span" style="font-size: medium;"><font class="Apple-style-span" color="#144FAE" face="Verdana" size="3"><span class="Apple-style-span" style="font-size: 13px;"><br></span></font></span></font></div></span></blockquote><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">The commands are:<br>tpbconv -s full180.tpr -f full180.trr -extend 5 -o edsam26-180f180.tpr -e full180.edr<br>aprun -n 60 $GROMACS_DIR/bin/mdrun -s edsam26-180f180.tpr -nosum -o edsam26-180f180.trr -x edsam26-180f180.xtc -ei edsamp26-180fit.edi -c edsam26-180f180.gro -e edsam26-180f180.edr -g edsam26-180f180.log<br><br>The ED sampling method I am using is linfix not radacc.<br><br>Thanks<br>Vijaya<br><br><br><hr>The New Busy think 9 to 5 is a cute idea. Combine multiple calendars with Hotmail.<span class="Apple-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" target="_new">Get busy.</a><span class="Apple-converted-space"> </span>--<span class="Apple-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="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="Apple-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="Apple-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; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-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; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br class="Apple-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="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></span>
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