replica_bias and colvars

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Thu Aug 10 2017 - 12:07:45 CDT

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

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