Re: ABF - coordNum collective variable

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Mar 16 2012 - 10:59:38 CDT

Hello Adam, the coordNum component does not have all the derivatives
implemented that are necessary to do ABF. If you absolutely need to
use it to compute a free energy, Jérôme can give you suggestions on
how to adapt it to ABF, or you can also try metadynamics.

Bests
Giacomo

On Thu, Mar 15, 2012 at 4:27 PM, Adam Skelton <mradamskelton_at_hotmail.com> wrote:
> Dear NAMD developers/experts,
>
> I was just wondering if the coordnum collective variable works at the moment
> (with ABF).
>
> I get this error message when I tried to use it in the same way I would with
> a distance collective variable.
>
> colvars:   Error: one or more of the components of colvar "COMDistance" does
> not support system force calculation.
> colvars:   If this error message is unclear, try recompiling with
> -DCOLVARS_DEBUG.
> FATAL ERROR: Error in the collective variables module: exiting.
>
> here is my input file
>
> colvar {
>   name COMDistance
> outputSystemForce no
> lowerboundary  0
>   upperboundary  10
>
>   lowerwallconstant 100
>   upperwallconstant 100
>
>
> coordNum {
> group1  {
> atomnumbers {44128 44129}
> }
> group2 {
> atomsFile             mid1.pdb
>  atomsCol              B
>  atomsColValue         1
> disableForces
> }
>
> }
> }
>
>
> abf {
> colvars COMDistance
> fullSamples 50
> }
>
> I am using the windows executable (NAMD_2.8_Win32-multicore), downloaded
> yesterday, but have run into similar problems with different versions too.
>
> I would appreciate any help, this would be a very useful collective variable
> for me!
>
> Thank you in Advance
>
> Adam
>
>

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