Re: Harmonic Constrain like MMFP in CHARMM

From: Vahid Mirjalili (mirjaliliv_at_gmail.com)
Date: Mon Jan 23 2012 - 14:56:55 CST

Hi again,

I read the documentation, this part about colvar -> rmsd is not clear to
me:
http://www.ks.uiuc.edu/Research/namd/2.7/ug/node49.html#SECTION0001221140000000000000
I don't know how I should define the atoms. I don't even know if it is
necessary to define the atoms like that, or just using the refPositionsFile
and refPositionsCol will work.
My colvar will be with rmsd as follows:

colvar {
   name rmsd
   width 1.0
   upperWall 1.0
   upperWallConstant 1.0
* rmsd {
      atoms {} ** not clear **
* refPositionsFile ref_file.pdb
      refPositionsCol B
      refPositionsColValue 1.0
* }*
}

On Sat, Jan 21, 2012 at 2:24 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:

> 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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