Tutorial-l Mailing List

From: DL Lynch (lynchdl_at_gmail.com)
Date: Fri Nov 03 2006 - 06:57:27 CST

Hi,

I ran the tutorial:
http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/

I built the system as described in the tutorial.
I minimized and equilibrated the systems as described in the tutorial
(equil.namd from the above website).

Then I ran the nptsim.namd. but instead of running for
run 20000 as described in the tutorial, i ran for 2ns (2000000).

When I did this the system seems to drift in the z direction. In the start
of the simulation the water's are equally spaced above and below the
bilayer,
however at the end of the 2ns (actually it doesn't take too long to see the
following effect, but I grabbed the last image) in 2ns_of_sim.png you can
see that the bilayer has "drifted" lower in the simulation cell. (P atoms
are the gold balls)

http://science.kennesaw.edu/~dlynch/2ns_of_sim.png
<http://science.kennesaw.edu/%7Edlynch/2ns_of_sim.png>

Do you have any thoughts as to what could be causing the
center of mass of the water to go "up" and the bilayer to go "down"?

Is this an issue of:
  1) poor equilibation from the equil.namd step? Meaning:
        a) the run where the protein is fixed is not long enough?
        b) and/or the run where it is constrained is not long enough?
        c) and/or the NPT with large damping coefs. is not long enough?
        d) and/or the damping coefs are made smaller (in the
nptsim.namdfile) in too bigh a step?
  2) the POPE are "seeing" each other in the periodic images?
  3) the peptide is "seeing" itself in the other images?

The reason I am trying to sort this out is that I am seeing a similar
behavior in
my simulations and so I tried the tutorial to see if I could sort out the
problem
on a smaller system.

I am going thru 1a-1d but I thought someone may have addressed this already.

Any thoughts or suggestions on this matter would be greatly appreciated.

Thanks!

ps This question has been touched on in the NAMD mailing list, but I was not
able to see
if it was resolved.

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