Re: How to extend an ABF simulation ?

From: horacio poblete (
Date: Tue Apr 30 2019 - 10:36:49 CDT

Hi Philippe.

This is an option, but with it you will start a “new” abf simulation from a previous one, what you are showing here is a good option (e.g.) if you want to modify your colvars file and extend or decrease your transition coordinate.

You can add a run number at the beginning of your namd configuration file:

set run 2
set outFile $name.$run
set last $name.[expr $run-1]

And you can read a restart colvars file using something like this to the Colvars section on your namd configuration file:

if {1} {
colvars on
colvarsConfig ../${colvarsConf}.colvars
if {$run > 1} {
    colvarsInput $last.restart.colvars.state

Now you can just increase your run number and restart easily your abf calculation.


Horacio Poblete Vilches PhD.
Principal Investigator
Center for Bioinformatics and Molecular Simulations
Escuela de Ingeneria en Bioinformática
Universidad de Talca
Phone: +56712203041

> On Apr 30, 2019, at 11:19 AM, philippe Bourly <> wrote:
> Hello everyone !
> I have a question about ABF simulations. I would like to extend my ABF simulation. I have extended the simulation the same way as a regular simulation and I have modified the abf block on the colvar file as the following:
> abf{
> colvars CycloAngle
> FullSamples 5000
> Historyfreq 2000
> inputPrefix output/cyclo
> }
> “cyclo” is the name of my previous simulation that I want to extend. Is it ok? Is it the good way to extend an ABF simulation?
> Best regards,
> Philippe

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