From: Reichert, David (reichertd_at_mir.wustl.edu)
Date: Fri Mar 05 2010 - 13:17:14 CST
I'm hoping someone can point me in the direction of better efficiency, here's the problem. I'm running ABF simulations of a small molecule in a lipid bilayer, where I calculate the PMF along the Z-axis of moving from the center of the bilayer to the surface. I build the system with the solute in the center, and do the usual steps ending with a 4ns equilibration run prior to starting the ABF runs. Now unsurprisingly during the 4 ns equilibration run the solute moves around, and by the end of some runs its drifted pretty far from the center of the bilayer which is where I want to start the ABF runs. Its trivial to pick our frames of the equilibration trajectory where it's close to the center, but the restart files are all for the end of the trajectory. I can save the coordinates from any given frame, but is it possible to also get the relevant velocity and xsc information in order to restart from that position? Or am I better off saving all of these files at more frequent intervals during the equilibration run and choosing the ones closest to where I'd want to start from ?
Thanks in advance,
David E. Reichert, PhD.
Asst. Professor of Radiology
Washington University School of Medicine
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