VMD-L Mailing List

From: Tessa Young (t.young5_at_student.unimelb.edu.au)
Date: Tue Nov 29 2011 - 23:06:25 CST

Thanks Axel, Jeffrey and Pablo for your help. We have managed to get the
trajectories written out by writing pdb files seperately as Axel suggested
- in this the pdb trajectories are primarily for visualisation purposes, so
the accuracy is not so important, but thanks for the heads up.

Tessa

On Tue, Nov 29, 2011 at 10:41 AM, Pablo M. De Biase
<pablodebiase_at_gmail.com>wrote:

> 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.
>>
>
>