ABF: Distances in colvars.traj not identical with VMD exported distances

From: Maximilian Ebert (max.ebert_at_me.com)
Date: Mon Oct 28 2013 - 16:21:45 CDT

Dear list,

I am running an ABF experiment using NAMD and the FF AMBER99SB-ildn. My colvars definition is added to the end of this email.

The atom numbers are the same as in the PDB file exported from tleap while preparing the system. After running the simulation I have the impression that I picked the wrong atom numbers. I imported the trajectory to VMD and exported the distances between the two atoms (I took into account that VMD starts at zero so that the distance is actually between 7426 and 7363). The distances do not match with the distances in the colvars.traj file. Is there any possibility to verify which atoms where really picked during the simulation? Since AMBER doesn’t use a PDB file as input in NAMD there is always the possibility that the atom numbering is wrong.

Thank you very much,


colvarsTrajFrequency 10000
colvarsRestartFrequency 10000

colvar {
   name AtomDistance
   width 0.5

   lowerboundary 3.0 ;# minimal distance
   upperboundary 32.5 ;# maximal distance

   lowerwallconstant 10.0 ;# provides the force constant. The energy unit of the constant is kcal/mol, while the spatial unit is that of the colvar.
   upperwallconstant 10.0 ;# same

   distance {
      group1 {
         atomnumbers { 7427 }
      group2 {
         atomnumbers { 7364 }

abf {
   colvars AtomDistance
   fullSamples 500 ;# Number of samples in a bin prior to application of the ABF

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