VMD-L Mailing List

From: Mark M Huntress (markmh_at_bgsu.edu)
Date: Sun Apr 03 2011 - 16:34:17 CDT

Hello,
  I am doing a classical MD trajectory of an organic molecule in a solvent box, and I am sampling frames (coordinates and velocities) from this MM trajectory to start new QMMM trajectories. For the frames that I am sampling, I am re-centering the solute in the solvent box (using pbc wrap -centersel {resid 1} -center com -compound res), and my concern is whether I can still use the velocities from the vel.dcd file. Will the coordinates and velocities be incompatible for any reason after I re-center? (for instance, reordering of solvent atoms or the velocities of some solvent atoms becoming in the wrong direction relative to the molecule?) Thanks,
Mark