From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Dec 18 2014 - 19:37:06 CST
Hello David,
1) please describe exactly the functional form
2) the order doesn't matter for the colvars' configuration
3) Outside alchemical transformations, FEP is still good but not as
convenient.
4) You can parallelize runs easily, you just specify different inputs. If
you're looking towards automating this, please consider trying the Tcl
commands recently included in NAMD 2.10.
On Wed, Dec 17, 2014 at 7:25 AM, David Huggins <djh210_at_cam.ac.uk> wrote:
>
> 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,
>
> Dave
>
>
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> 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
> Email: djh210_at_cam.ac.uk
> Web: http://www.tcm.phy.cam.ac.uk/~djh210/
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
-- Giacomo Fiorin Assistant Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 https://icms.cst.temple.edu/members.html http://giacomofiorin.github.io/
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:29 CST