Re: How to extend an ABF simulation ?

From: philippe Bourly (philippe.bourly20_at_gmail.com)
Date: Wed May 01 2019 - 02:55:29 CDT

Thank you, this is very helpful!

Best,
Philippe

On Tue, Apr 30, 2019 at 5:36 PM horacio poblete <elhoraki_at_gmail.com> wrote:

> 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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