Re: replica_bias and colvars

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Aug 10 2017 - 12:51:26 CDT

Hi JC, how is this code calling Colvars? I don't see any Tcl command that
does call it in there.

The primary method for changing parameters for a bias should be through the
"cv" command. Deleting the bias and re-creating it with the new
configuration would be the way to go.

Giacomo

On Thu, Aug 10, 2017 at 1:07 PM, JC Gumbart <gumbart_at_physics.gatech.edu>
wrote:

> Has something changed in newer versions of NAMD with regards to how inputs
> are fed to different replicas in colvars?
>
> Specifically, the input below worked fine in earlier versions (2.10 I
> think?), but in 2.12, the center and forceConstant both get set to the same
> value, namely that for the center.
>
> > proc replica_bias { i } {
> > set c [expr 5.5 + $i*0.5]
> > set klist { 10 10 10 10 10 10 5 5 5 5 5 5 5 5 5 5 5 5 5 5 }
> > set k [expr [lindex $klist $i]*0.05*0.05]
> > return [list Z "centers \{$c\} forceConstant \{$k\}"]
> > }
>
> And then this is how that proc is used:
> > set replica(colvarbias) [replica_bias $replica(index)]
> > for { set i 0 } { $i < $replica(num_neighbors) } { incr i } {
> > set replica(colvarbias.$i) [replica_bias $replica(index.$i)]
> > set replica(colvarbias.$i) [replica_bias $replica(index.$i)]
> > }
>
>
> Thanks!
> JC
>
>

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

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