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Hi<br>I need some information about how ED sampling works when <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><br>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. <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></body>
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