Removing minima and transition states from the database

Sometimes it is necessary to remove certain stationary points from the database files. Deleting the files by hand will damage the numbering schemes within the pathsample databases, therefore use the keyword REMOVESP.

First off back up the directory.

The minima specified in files min.remove and ts.remove are removed and new files min.data.removed, ts.data.removed, min.A.removed, min.B.removed, points.min.removed and points.ts.removed are created with a consistent numbering scheme for the remaining stationary points. The first lines of min.remove and ts.remove must contain a single integer, which is the number of stationary points listed for removal on the remaining lines. Pathsample with not remove the minima without their connected transition states. If pathsample fails these transition states will be listed in the output. Simply add them to ts.remove and run it again.

A potential gotcha occurs when the minimum to be removed is the only minimum in the A or B minima, because it is considered an error to remove all the A minima or all the B minima. If you are indeed trying to remove your only A minimum then obviously you cannot continue a pathsample run. So first, you'd better add an alternative A minimum that you're not going to remove to the A set. Also the lists min.A and min.B need to be mutually exclusive. If you are removing minimum 1, just change min.A to

  2
  1
  2

After the database have been correctly renumbered, move the database files back to there proper places via,

  mv min.data.removed min.data 
  mv ts.data.removed ts.data
  mv points.min.removed points.min
  mv points.ts.removed points.ts
  mv min.A.removed min.A
  mv min.B.removed min.B

Also the pairs list is no longer accurate and needs to be removed.

  rm pairs.data

You should be able to restart pathsample with the databases numbered properly.

--mp466 02:05, 24 October 2008 (BST)