From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Jun 15 2012 - 01:34:42 CDT
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Axel Kohlmeyer
> Gesendet: Freitag, 15. Juni 2012 04:50
> An: Dr. Eddie
> Cc: namd-l_at_ks.uiuc.edu
> Betreff: Re: namd-l: minimization and water bubbles
> On Thu, Jun 14, 2012 at 10:33 PM, Dr. Eddie <eackad_at_gmail.com> wrote:
> > Hi all,
> > I have a small (2700 atom) protein that is solvated and should be
> very close
> > to correctly folded. When I run the minimization on the solvated
> system it
> > seems to form a large air bubble. I am using pbc and waterWrap on and
> at the
> > end of my config file it has:
> > minimize 800
> > reinitvels 310
> > run 20000000
> > In the output from the run after the energy it prints:
> > REINITIALIZING VELOCITIES AT STEP 800 TO 310 KELVIN.
> > Yet the protein seems to be very cold and there is a large air bubble
> in the
> > system. This is not the "fake" bubble due to pbc (I see that one as
> > Even after 2 ns the bubble is still almost perfectly spherical.
> Shouldn't it
> > have reheated and given me something similar to when I don't
> minimize? Has
> > anyone had this problem and knows what I am doing incorrectly?
> you are probably running with constant volume.
> check your system's density, almost all tools to
> solvate molecules leave some little vacuum to
> avoid overlaps (which will lead to atoms being
> "shot" through the simulation cell and the simulation
> crashing). if you run long enough with constant
> volume, you'll get a little vacuum bubble.
Means that you should start a pressure controlled run to remove the bubble
(let box shrink).
> > The protein's structure is almost identical after minimization yet
> there is
> > a large change in pressure and potential energy during minimization
> so I
> > assume almost all the minimization is coming from the water. Also I
> > see the bubble when I don't minimize.
> > I greatly appreciate any help. Thanks in advance!
> > Eddie
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:08 CST