dummyAtom in distance colvar in ABF calculations

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Sat May 12 2018 - 16:44:16 CDT

Hi all,

I am using distance colvar for ABF calculations and I want to use dummyAtom
for my group 2 atoms that coincides with the COM of the protein (instead of
calculating COM of the whole protein every step). I am getting the
following error:

colvars: Errcolvars: Error: total total forces are not available from a
dummy atom group.
colvars: No such file or directory
FATAL ERROR: Error in the collective variables module: No such file or
directory
or: total total forces are not available from a dummy atom group

Here is my .in file:

colvarsTrajFrequency 500
colvarsRestartFrequency 5000

colvar {
   name IonDistance

   width 0.1

   lowerboundary 70.0
   upperboundary 74.0

   lowerwallconstant 100.0
   upperwallconstant 100.0

   distance {
      group1 {
         atomnumbers { 66462 }
      }
      group2 {
         dummyAtom (1.485 -0.486 -0.418) }
   }
}

abf {
  colvars IonDistance
  fullSamples 500
  hideJacobian
}

Is this the right way to refer to the dummyAtom? I would appreciate your
help!

Thank you,

Olga

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