Re: NAMD 2.7b1 distanceDir

From: Guanglei Cui (amber.mail.archive_at_gmail.com)
Date: Mon May 10 2010 - 11:04:25 CDT

Hi Giacomo,

That might have been the case, since the colvar definition file was
copied over from an older calculation. Thank you very much.

Cheers,
Guanglei

On Fri, May 7, 2010 at 6:16 PM, Giacomo Fiorin
<giacomo.fiorin_at_temple.edu> wrote:
> Hi Guanglei, did you enable outputSystemForce by any chance?  As specified
> in the documentation, that's just not available for distanceDir, only for
> distance, distanceZ, distanceXY.
>
> I tried it out, since you said you were playing with it starting from
> "distance", and got the error message that you posted.  The message is
> misleading, because it complains about a forbidden operation.  What should
> be printed, instead, is that distanceDir doesn't support outputSystemForce,
> period.  Sorry about the confusion.
>
> I'll fix the error message in the next CVS update.
>
> Giacomo
>
> ---- ----
> Giacomo Fiorin
>   ICMS - Institute for Computational Molecular Science
>     Temple University
>     1900 N 12 th Street, Philadelphia, PA 19122
> mail:    giacomo.fiorin_at_gmail.com
> ---- ----
>
>
> On Fri, May 7, 2010 at 1:02 PM, Guanglei Cui <amber.mail.archive_at_gmail.com>
> wrote:
>>
>> Hi Giacomo,
>>
>> thanks for the reply. Actually, I wasn't manipulating the vector, but
>> wanted to monitor it. I think I also tried 2.7b2, but got the same
>> error. Unfortunately, I removed the colvar definition file. The colvar
>> was defined by two groups of atoms, and it worked fine if the type was
>> changed from distancedir to distance. So, it wasn't a syntax error.
>>
>> Thanks again,
>>
>> Regards,
>> Guanglei
>>
>> On Thu, May 6, 2010 at 6:22 PM, Giacomo Fiorin
>> <giacomo.fiorin_at_temple.edu> wrote:
>> > Hi Guanglei, the error is raised because the value of the colvar is
>> > copied
>> > from one place to the other.  The plural refers to the values, not the
>> > colvar.
>> >
>> > Depending on what you're trying to do, some things may or may not be
>> > supported, because distanceDir is not a scalar number, it's a
>> > 3-dimensional
>> > vector with norm 1.  What you can do is to apply harmonic constraints,
>> > optionally moving, and perform metadynamics, although there is no
>> > function
>> > yet to automatically project the results onto a grid for visualization
>> > purposes.
>> >
>> > If you find that the error message occurs no matter what you do, it
>> > should
>> > be because of a bug that was fixed in NAMD 2.7b2.
>> >
>> > Bests
>> > Giacomo
>> >
>> > ---- ----
>> > Giacomo Fiorin
>> >   ICMS - Institute for Computational Molecular Science
>> >     Temple University
>> >     1900 N 12 th Street, Philadelphia, PA 19122
>> > mail:    giacomo.fiorin_at_gmail.com
>> > ---- ----
>> >
>> >
>> > On Thu, May 6, 2010 at 2:03 PM, Guanglei Cui
>> > <amber.mail.archive_at_gmail.com>
>> > wrote:
>> >>
>> >> Hi there,
>> >>
>> >> I'm playing with the colvar type distanceDir in namd 2.7b1, but I got
>> >> an error of the following:
>> >>
>> >> colvars: x1 type=3, x2 type=1
>> >> colvars: Performing an operation between two colvar values with
>> >> different types ...
>> >>
>> >> I'm a little puzzled as there is only colvar defined in the input. Has
>> >> anyone noticed this?
>> >>
>> >> Thanks in advance,
>> >>
>> >> --
>> >> Guanglei Cui
>> >>
>> >
>> >
>>
>>
>>
>> --
>> Guanglei Cui
>>
>
>

-- 
Guanglei Cui

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