Re: How to extend an ABF simulation ?

From: horacio poblete (elhoraki_at_gmail.com)
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.

Best!

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

> On Apr 30, 2019, at 11:19 AM, philippe Bourly <philippe.bourly20_at_gmail.com> 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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