CCL



Dear CCLers,
 Happy new year!
 I have one question for CHARMm about equilibration. Generally, the
 calculation is started from the X ray structure, then heating,
 equilibrating by velocity scale, and lastly production run without
 velocity scale in the NVE MD simulation. However, I found that many of the
 authors do not check the system to make sure it has been equilibrated
 before they take the production run. Fro example, Some authors observe the
 temperature  is increasing with the potential energy drifting down in the
 production run. However, they still do the analysis. Is that a problem?
 Thanks for all your help,
 Wei Shi