From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jan 24 2012 - 09:40:08 CST
No problem.
Please keep in mind this important distinction.
The *tutorial* will get you started with the basics of one specific example.
The *user's guide* is the only complete reference to the rest of the
features.
On Mon, Jan 23, 2012 at 5:38 PM, Vahid Mirjalili <mirjaliliv_at_gmail.com>wrote:
> Hi Giacomo, the problem resolved, sorry for sending too many messages, it
> was really difficult to find out the atoms group definition in the
> tutorial, until I searched in the PDF version instead of the on-line version
>
> Thanks
>
>
> On Mon, Jan 23, 2012 at 3:56 PM, Vahid Mirjalili <mirjaliliv_at_gmail.com>wrote:
>
>> 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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