VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat Apr 25 2020 - 19:51:01 CDT

Oh okay, the name "harm1" sounded more like a harmonic restraint :-) You
did mention the presence of walls.

Giacomo

On Sat, Apr 25, 2020 at 8:35 PM Pant, Shashank <pant5_at_illinois.edu> wrote:

> Hi Giacomo,
>
> I think I didn’t understand your question on restraint and metadynamics
> energy. My metadynamics block was:
>
> metadynamics {
> name harm1
> colvars 11 21
> hillWeight 0.25
> hillWidth 1.5
> keepHills on
> wellTempered on
> biasTemperature 6000
> newHillFrequency 1000 # Default is 100 - lower numbers = faster
> }
>
> So, I decide to use *cv bias harm1 energy*
> Is it correct? Or there something more to it which I probably didnt
> understand.
>
> I can put some comments in my script and will share it you so that we can
> put it in COLVR repository.
>
> Thanks
> Shashank
>
> On Apr 24, 2020, at 1:37 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
> *cv load old.state*
> *set file [open "biasA.dat" w]*
> *set numframe [molinfo top get numframes]*
> *for {set f 0} { $f <= $numframe } {incr f} {*
> *cv frame $f*
> *cv update*
> *set mtd [cv bias metadynamics1 energy]*
> *set bb [cv bias harm1 energy]*
> *puts $file "[expr $f*0.1] [expr $bb + $mtd]”*
> *}*
>
>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin