Implementing the Virtual Bond Algorithm Using Colvars

From: David Huggins (
Date: Wed Dec 17 2014 - 06:25:33 CST

Dear All,

I am currently attempting to compute the free energy of attaching six
restraints to a protein-ligand complex, following the Virtual Bond
Algorithm (VBA) method. I have a few queries to clarify things:

1) My understanding is that this can be done using colvars but cant be done
using extrabonds?
2) For the best results using colvars, should the restraints be introduced
together or one after another?
3) The free energy change can be estimated by TI using a lambdaSchedule in
the colvars file, but can this be achieved using FEP as well?
4) Can the process be parallelised by setting a different lambdaSchedule
in different colvars files? I note that the lambdaSchedule needs at least
two values to be specified.

Thanks very much for any help,



Dr David J. Huggins
MRC New Investigator
Theory of Condensed Matter Group
Cavendish Laboratory
JJ Thomson Avenue
Cambridge, CB3 0HE
United Kingdom

Phone: +44 (0)1223 766397 or +44 (0)1223 337278
Fax: +44 (0)1223 337356


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