Re: Colvars: Using "Alpha" Component

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Sep 24 2010 - 03:27:40 CDT

Hi Alex,

By "system force", the colvar module means "a projection of the forces
acting on the atoms onto the collective variable". This is really useful for
ABF simulations only: the only reason you are getting the error here is
because you explicitly requested that quantity as an output.

Cheers,
Jerome

On 24 September 2010 02:26, Alexander Predeus <predeus_at_gmail.com> wrote:

> Hello All,
>
> I'm interested in using a collective variable based on "alpha"
> component of colvar module, and I am running into some kind of
> persistent error. The message is as follows:
>
> > Error: one or more of the components of colvar "a1" is unable to
> calculate system forces.
>
> The error persists when I'm using both 2.7b3 and 2.7b4 versions, and
> two very different systems (~ 500k atoms and ~ 20k atoms). The colvar
> config file is listed next:
>
> colvarsTrajFrequency 10
>
> colvar {
> name a1
> width 1.0
> outputVelocity on
> outputAppliedForce on
> outputSystemForce on
> alpha {
> residueRange 1068-1075
> psfSegID PROA
> }
> }
>
> harmonic {
> colvars a1
> forceConstant 50
> centers 0.5
> #targets 1.0
> #targetsNumSteps 2000
> }
>
> I've tried playing with other parameters that one can change for alpha
> component and nothing seems to help me get rid of this error. I've
> also compiled NAMD with -DCOLVARS_DEBUG option, which does make it a
> lot more talkative, but doesn't help in this particular case; the
> error message remains the same.
>
> Any suggestions would be appreciated.
>
> -- Alex Predeus
> Michigan State University
>
>

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