From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Fri May 07 2010 - 17:16:31 CDT
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
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:06 CST