From: Angelo Rossi (angelo.raymond.rossi_at_gmail.com)
Date: Sun Jan 30 2011 - 11:00:38 CST
Dear Jerome:
It looks like a problem with the way the colvar is defined. Most
> probably, the sets of atoms for either the "ref" or "main" groups is
> not what you intended. The value of the colvar at time zero (here, 46
> A) should be exactly what you expect from the setup. To troubleshoot
> this, check the colvars log as part of the NAMD standard output. Are
> the total masses of each atom group correct? If you visualize group
> "main" in VMD, remember that VMD uses 0-based indices while NAMD uses
> 1-based atom numbers (in VMD, they are called "serial"). You can also
> visualize the reference group in VMD by loading the PDB file and
> coloring the display by beta value.
>
Thank you for your help. I think I figured it out.
I am using periodic boundary conditions for the lipid bilayer
-----------------------------------------
ref
z-axis
main / |\
----------------------------------------- |
ref |
|
|
main |
-----------------------------------------
ref
main
-----------------------------------------
So the distance value was returned according to the minimum-image
convention. Because the ref of one unit cell is closest to the main of
another, I was seeing the effect I described.
I resubmitted the calculation with *forceNoPBC yes*, and I seem to be
getting the correct behavior which allows the z-distance projection to be
obtained from the coordinates of the internal cell. Why didn't I think of
this before writing my note and clogging the NAMD-l mailing list. Duh!
The output so far included in the .traj file is:
# step ProjectionZ
0 -6.10002799457780e+01
100 -5.87957071710544e+01
200 -5.60513774031392e+01
300 -5.32740735724076e+01
400 -5.05244950580049e+01
500 -4.79259377290209e+01
600 -4.54869867386761e+01
700 -4.29729090456969e+01
800 -4.05310926821628e+01
900 -3.82291241548357e+01
1000 -3.58880194484213e+01
Thanks so much for having the foresight to include this ability into the
colvars module.
Best regards,
Angelo
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