From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Aug 10 2017 - 15:25:35 CDT
The deprecated NAMD command "colvarbias" is still supported by the latest
snapshots of NAMD and Colvars.
Giacomo
On Thu, Aug 10, 2017 at 1:58 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:
> The old way would have been through something like "eval colvarbias [cat
> changeconfig somestuff here]". I ran into problems once when I neglected to
> change the name of the harmonic bias I wanted to change (I call all of mine
> harm), accidentally using the collective variable the harmonic was trying
> to bias as the name instead. Is "Z" the name of your collective variable or
> the harmonic that biases the collective variable?
>
> -Josh
>
> On 08/10/2017 11:54 AM, Giacomo Fiorin wrote:
> 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<ma
> ilto: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
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>
>
>
-- 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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