Re: Help With colvars/abf Please

From: Angelo Rossi (
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


                  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,


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