From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Sat Aug 12 2017 - 06:49:35 CDT
After further digging with Giacomo’s help, the solution turned out to be so simple:
> return [list Z "centers \{$c\} forceConstant \{$k\}”]
is replaced with
> return [list Z "centers \{$c\}\nforceConstant \{$k\}”]
(note the newline)
Apparently the latter one is the way it was always supposed to be, but for some reason the former way worked in earlier versions. Thanks for helping us track it down!
Best,
JC
> On Aug 10, 2017, at 10:10 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:
>
> The syntax of the colvarbias command that Josh quoted:
> eval colvarbias [concat changeconfig $replica(colvarbias)]
> has not changed.
>
> Perhaps what changed is how the replica dictionary is filled in, i.e. the problem is in the script.
>
> Giacomo
>
> On Thu, Aug 10, 2017 at 5:17 PM, JC Gumbart <gumbart_at_physics.gatech.edu <mailto:gumbart_at_physics.gatech.edu>> wrote:
> Z is the name of the harmonic restraint.
>
> For reference, the colvar is in a different file:
>
> harmonic {
> name Z
> colvars COMDistance
> forceConstant { 0.0125 } centers { 0.0 }
> }
>
> But the replica(colvarbias.$i) is how the script tells namd to update that replica's properties. I wondered if something has changed in how namd interprets that data.
>
> Thanks!
> JC
>
>
> On Thu, Aug 10, 2017, 1:58 PM Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov <mailto: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 <mailto:gumbart_at_physics.gatech.edu><mailto:gumbart_at_physics.gatech.edu <mailto: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
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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 <http://goo.gl/Q3TBQU>
> https://github.com/giacomofiorin <https://github.com/giacomofiorin>
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