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I am trying to use trjconv to generate a new .xtc file in which all frames have been aligned based on a subset of atoms (e.g. I have a multi-domain protein and I want to align the trajectory to one of the domains). Using a standard .ndx file only outputs the atoms associated with the fitted domain. I was wondering if there is a straightforward way to do what I describe without having to hack trjconv?<div><br></div><div>Looking at the source for do_fit.c it looks like if I were to set the mass of atoms that I didn't want to use in the alignment to zero, then it might work, but I am generally trying to avoid having to generate a tpr file since I'm coming from the pdb/psf world. </div><div><br></div><div>Any suggestions would be appreciated.</div><div><br></div><div>Josh<br><br><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------------------------------------</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Joshua L. Adelman</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Biophysics Graduate Group Lab: 510.643.2159</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">218 Wellman Hall Fax: 510.642.7428</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">University of California, Berkeley <a href="http://nature.berkeley.edu/~jadelman">http://nature.berkeley.edu/~jadelman</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Berkeley, CA 94720 USA <a href="mailto:jadelman@berkeley.edu">jadelman@berkeley.edu</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">------------------------------------------------------------------------------------------------------</div><br class="Apple-interchange-newline"></span> </div><br></div></body></html>