Re: Harmonic Constrain like MMFP in CHARMM

From: Vahid Mirjalili (
Date: Fri Jan 20 2012 - 19:41:28 CST

ok, so I am trying to write a colvar config file (please see the attached),
and I also add these two lines to the main NAMD confg file:

colvars on
colvarsConfig rmsd

But when I run this, it gives me this error:

But NAMD crashes and exits, with this error message:

colvars: Error: no collective variables defined.
colvars: If this error message is unclear, try recompiling with
FATAL ERROR: Error in the collective variables module: exiting.

I don't understand why it doesn't recognize the colvar that I have declared?

Any idea?

Vahid Mirjalili
Michigan State University

On Fri, Jan 20, 2012 at 7:42 PM, Giacomo Fiorin <>wrote:

> upperBoundary, defined for a distanceXY variable?
> On Fri, Jan 20, 2012 at 6:52 PM, Vahid Mirjalili <>wrote:
>> Dear all,
>> I am a new NAMD user, and I want to apply a constrain potential which
>> will only apply if the value of colvar is greater than a certain limit.
>> This is similar to MMFP in CHARMM, like for example when we apply a
>> harmonic cylindrical potential with outside option,
>> so that only if |r-roff| > 0 the harmonic energy (r-roff)^2 and the
>> corresponding force will be evaluated
>> Is this possible to do this with NAMD or it needs implementation?
>> Thanks,
>> Vahid Mirjalili
>> Michigan State University

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