From: Pablo M. De Biase (pablodebiase_at_gmail.com)
Date: Mon Nov 28 2011 - 17:41:40 CST

You are right, is independent of the origin but it is dependent on the
orientation. I had problems because I was using an irregular box. If you
can save each vector in the xst that may solve the problem (depending on
the case). Anyway I think that a new dcd format must be formulated to solve
this kind of issues. Is not a big deal to include 3 or more real numbers in
the dcd format so to have all the information of the vectors (I mean 9 real
numbers to build the matrix) and maybe the origin (3 reals more). This is
what I did without compromising the performance of the program.

On Mon, Nov 28, 2011 at 4:13 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Mon, Nov 28, 2011 at 5:11 PM, Pablo M. De Biase
> <pablodebiase_at_gmail.com> wrote:
> > If you are using constant pressure the box vectors are changing all the
> time
> > because the volume is fluctuating. So the vectors you have in the xst
> file
> > is only useful for the first frame not for the rest. If you are trying to
> > replicate the box with the correct box vectors you'll have to do
> something
> > similar to what I did.
>
> no. periodic box replication is independent of the origin
> and in NAMD/CHARMM it is guaranteed that the first
> vector is always along the x-axis, the second in the
> xy-plane and that you have a right-handed coordinate
> system. thus information in the .dcd file is sufficient.
>
> only if you want to allow arbitrary box vector orientations,
> like they are used in condensed matter DFT calculations
> (for efficiency reasons), then you have a problem with
> this information. this is the reason why the molfile plugins
> for gaussian cube files and .xsf files rotate the box (and
> the enclosed coordinates and grids) to match the
> conventions from above.
>
> cheers,
> axel.
> >
> > On Mon, Nov 28, 2011 at 2:00 PM, Jeffrey Potoff <jpotoffx_at_gmail.com>
> wrote:
> >>
> >> On 11/28/2011 12:45 PM, Axel Kohlmeyer wrote:
> >>>
> >>> On Mon, Nov 28, 2011 at 2:20 AM, Tessa Young
> >>> <t.young5_at_student.unimelb.edu.au> wrote:
> >>>>
> >>>> Dear fellow vmd users,
> >>>>
> >>>> I have been using catdcd (version 4.0b) to create pdb trajectory files
> >>>> from
> >>>> namd dcd trajectory files. I have run constant pressure simulations
> >>>> (using
> >>>> periodic boundary conditions) with a varying periodic cell size.
> However
> >>>> when I use catdcd, the periodic cell size is only written out for the
> >>>> first
> >>>> frame and not for the following frames in the trajectory. Hence I have
> >>>> lost
> >>>> the periodic boundary information in the pdb output.
> >>>
> >>> you also lost a lot of precision of your coordinate information.
> >>>
> >>>> Is it possible to write out the cell size at the beginning of each pdb
> >>>> frame
> >>>> in the trajectory, using catdcd?
> >>>
> >>> only if you write out individual .pdb files for each frame and then
> >>> concatenate them together, e.g. using "cat". the CRYST1 record
> >>> is not written in the molfile function that writes out the coordinates.
> >>>
> >>> overall, writing out .pdb trajectories should be avoided as much
> >>> as possible due to the massive loss of coordinate detail.
> >>>
> >>
> >> Apparently I missed the original post...if one is determined to
> generate a
> >> bunch of PDB files, then it should not be too much of a stretch to
> write a
> >> shell script that grabs the cell vector data from the XST file and
> merges it
> >> with each PDB file.
> >>
> >> Agree with Axel, though. One is almost always better off working
> >> directly with the DCD file.
> >>
> >> Regards,
> >> Jeff
> >>
> >> --
> >> =================================================================
> >> Jeffrey J. Potoff jpotoff_at_wayne.edu
> >> Associate Professor Wayne State University
> >>
> >> Department of Chemical Engineering and Materials Science
> >> 5050 Anthony Wayne Dr Phone:(313)577-9357
> >>
> >> Detroit, MI 48202 Fax: (313)578-5815
> >> http://potoff1.eng.wayne.edu
> >> =================================================================
> >>
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>