Re: restarting a simulation ?

From: Chris Harrison (
Date: Wed Mar 17 2010 - 00:39:27 CDT


If I understand the question correctly, you'll want to re-run and save to
your output files (xsc and dcd w/ velocities) more frequently. Please make
sure to look into the "velDCDfile" command in the NAMD userguide (


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078
On Fri, Mar 5, 2010 at 2:17 PM, Reichert, David <>wrote:
>  Hi all,
> Iím hoping someone can point me in the direction of better efficiency,
> hereís the problem. Iím 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
> itís 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 Iíd want to start from ?
> Thanks in advance,
> -david
> David E. Reichert, PhD.
> Asst. Professor of Radiology
> Washington University School of Medicine
> e-mail:
> voice: 314-362-8461
> fax: 314-362-9940
> web:
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