ABF for dihedrals

From: Albers, Thomas (TALBERS_at_augusta.edu)
Date: Thu Aug 03 2017 - 12:48:24 CDT

Hello!

I would like to explore the energy profile of the conformational change in a turn in my protein. The Ramachandran angle phi varies from 50 to 260 degrees in that system; the range between -100 and 50 degrees is not visited.

The interval for dihedral angles in NAMD is -180 - 180 degrees. How to get around the periodicity issue, because as far as I can see the interval beyond 180 deg, where the angle wraps around, is not reached. Here is an excerpt from the .count file:

..

 172.5 15805
 177.5 13467
 182.5 0
 187.5 0
..

The colvar is defined like this:

colvar {
  name phi265

  width 5.0
  lowerboundary 50
  upperboundary 260
  lowerWallConstant 0.2
  upperWallConstant 0.2

  dihedral {
    group1 { atomNumbers 4365 }
    group2 { atomNumbers 4367 }
    group3 { atomNumbers 4369 }
    group4 { atomNumbers 4372 }
  }
}

abf {
 colvars phi265
}

How to get around the wraparound issue?

Thanks,
Thomas

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