From: Shaon Chakrabarti (shaonc_at_gmail.com)
Date: Wed May 23 2012 - 14:48:35 CDT
Hi NAMD experts,
I'm facing two problems with the gyration component in
the Colvars module.
1) The NAMD user's guide says that the radius of gyration
is defined using the Center of Geometry. However, when
I write my own code (using the COG definition) to compute
the Rg of a molecule, the Rg value is always about 0.2
angstroms more compared to the output in the 'colvars.traj'
file. The values from my code exactly match the values
I get if I use the 'measure rgyr' command in VMD. I also
computed Rg using Center of Mass, but that makes the
difference even larger. I'd be grateful if someone can tell
me if I'm making a mistake somewhere, or if Rg is
actually defined differently in the Colvars module.
P.S. My molecule (about 30 angstroms long when fully
extended) is in the middle of a water box of side 55
2) The second problem is similar (as I understand from
the threads in 2008) to what Subramanian
Vaitheeswaran faced while using the gyration
component with ABF. If I specify the Rg to be (say)
within say 5 and 7 angstroms, and use ABF to get
the PMF, the system hovers at Rg value around
4.5-4.8 most of the time! A final resolution doesn't
seem to have been posted back in 2008, and it
would be of immense help if someone could tell
me what's going on....if the problem has been
resolved. I tried switching the hideJacobian option
to yes, and increasing the lower and upper wall
constants, but these don't make any difference.
It would be great if someone could help with these two issues.
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