VMD-L Mailing List

From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Mon Nov 28 2011 - 16:30:08 CST

On 11/28/2011 5:10 PM, Pablo M. De Biase 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.

Why? The cell basis vectors are updated in the XST file as the
simulation runs as long as you tell NAMD to output the data.

>
> On Mon, Nov 28, 2011 at 2:00 PM, Jeffrey Potoff <jpotoffx_at_gmail.com
> <mailto: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
> <mailto: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 <mailto:jpotoff_at_wayne.edu>
> Associate Professor Wayne State University
> Department of Chemical Engineering and Materials Science
> 5050 Anthony Wayne Dr Phone:(313)577-9357
> <tel:%28313%29577-9357>
> Detroit, MI 48202 Fax: (313)578-5815
> <tel:%28313%29578-5815>
> http://potoff1.eng.wayne.edu
> =================================================================
>
> 

-- 
=================================================================
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
=================================================================