VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 11 2010 - 22:01:11 CDT

On Wed, Aug 11, 2010 at 9:59 PM, Cun Zhang <apzc2529_at_gmail.com> wrote:
> Hi,all
> I have some problems when I deal with lammpstrj files in vmd.

please explain what the problem with lammpstrj is,
you only show fragments from .pdb files below.

> I found the index of atoms will change to the line number of atoms
> when the line number of atoms are not same as the index of atoms.
> e.g.

that is not correct. the .pdb reader simply ignores the atom
index on reading, since this is not a global index but only
within a segment. your file isn't really a standard conforming
.pdb file. the ATOM record is reserved for know standard
residues.

> a sequence from a pdb file as following:
> ATOM      1  C   UNK     1     102.970  86.780  51.730  1.00  0.00
> C
> ATOM      3  C   UNK     1     102.580  91.020  51.730  1.00  0.00
> C
> ATOM      2  C   UNK     1     102.930  88.200  51.730  1.00  0.00
> C
> ATOM      4  C   UNK     1     102.280  92.400  51.730  1.00  0.00
> C
>
> when I import it into vmd, it will change to
>
> ATOM      1  C   UNK     1     102.970  86.780  51.730  1.00  0.00
> C
> ATOM      2  C   UNK     1     102.580  91.020  51.730  1.00  0.00
> C
> ATOM      3  C   UNK     1     102.930  88.200  51.730  1.00  0.00
> C
> ATOM      4  C   UNK     1     102.280  92.400  51.730  1.00  0.00
> C

it is the common convention to consider two .pdb files
to be the same, if the atoms are the same and in the same
order.

> I test pdb file and lammpstrj file, return the same result.

lammps dump files will be written in unspecified order
when written by a parallel version of LAMMPS, so sorting
atoms upon reading by the atom tag is a necessity to
maintain consistency within a single file and between
multiple files.

> Except Re-ordering the pdb file, is there any way to fix it?

fix what? to what? and for which format?

axrel.

> Thank you!
>
> Cun Zhang
>
> --
> Blog: http://www.edwardpku.com/cun
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.