From: Hyuntae Na (htna_at_hotmail.com)
Date: Wed Jun 27 2012 - 20:22:15 CDT
I just modified some of the setting from the configuration of "ubq_wb_eq.conf" in the tutorial file. I also run the simulation in the namd tutorial files, but the same phenomenon happens.
How can I reset the "position restraints" from my configuration file?
> Date: Tue, 26 Jun 2012 10:03:34 +0200
> From: tillmann.utesch_at_mail.tu-berlin.de
> Subject: RE: AW: AW: namd-l: Sudden energy drop after minimization
> Did you remove position restraints from your system after the minimization?
> Quoting Hyuntae Na <htna_at_hotmail.com>:
> > Hi, I agree that I should take longer minimization steps than 300. I
> > tested the 20,000 minimization step. After its minimization
> > iteration takes around 10,000 steps (the half of 20,000), the
> > protein in the water box is almost reached to its minimum structure
> > (its conformation does not change much except small fluctuation). By
> > the way, after the minimization with 20,000 steps is fully done, the
> > energy drop still exists. In this case, should the minimization be
> > continued until there is no atom movement at all? One my question is
> > if the MD simulation test example in the tutorial files,
> > "namd-tutorial-files\1-3-box", runs with improper minimization,
> > because its log also shows the same bond energy drop : 605.1437 ->
> > 81.9360.
> > Thank you very much. Best regards,--Hyuntae
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