From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat Jan 21 2012 - 01:24:14 CST
Hello Vahid, a good idea would be to write the configuration file in which
you're defining the variables, and pass the name of that file as an
argument to colvarsConfig.
Of course, this is all documented in the user's guide. If you find
something not clear in there, feel free to ask for clarification.
But please, first read the manual.
Giacomo
On Fri, Jan 20, 2012 at 8:41 PM, Vahid Mirjalili <mirjaliliv_at_gmail.com>wrote:
> 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
> -DCOLVARS_DEBUG.
> 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?
>
> thanks
>
> Vahid Mirjalili
> Michigan State University
>
> On Fri, Jan 20, 2012 at 7:42 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:
>
>> upperBoundary, defined for a distanceXY variable?
>>
>>
>> On Fri, Jan 20, 2012 at 6:52 PM, Vahid Mirjalili <mirjaliliv_at_gmail.com>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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