VMD-L Mailing List

From: Cun Zhang (apzc2529_at_gmail.com)
Date: Thu Aug 12 2010 - 03:52:10 CDT

On Thu, Aug 12, 2010 at 11:01 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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'm trying deal with lammpstrj file with vmd script, but can't obtain the
right data( e.g. obtain the center of "index 0 to 23").
And I checked my script,it's ok. Finally, I found "index 0 to 23" isn't the
same as atoms in the initial data file. The Index of Atoms
are re-ordered as the order of the data.Here is a example:

ITEM: TIMESTEP
5000
ITEM: NUMBER OF ATOMS
234
ITEM: BOX BOUNDS
-99.9998 99.9998
-99.9993 99.9993
-0.0103184 400.01
ITEM: ATOMS id type xs ys zs
23 1 0.486681 0.494531 0.00251958
24 1 0.489859 0.489456 0.00418073
25 1 0.493987 0.484196 0.0026156
36 1 0.486359 0.495119 0.00966315
....
1 1 0.51566 0.5 0
.... (and so on)

This is a lammpstrj fragments. ATOM index 23 is the first ATOM data:
23 1 0.486681 0.494531 0.00251958
After loading this lammpstrj file, the index of this atom will become 1.
You can verify it through the following commands:
vmd > measure center [atomselect top "index 0"]
-2.6637954711914063 -1.0937881469726563 0.9975647926330566
vmd > expr 99.9998*2*0.486681-99.9998
-2.6637946724000017
vmd> expr 99.9998*2*0.494531-99.9998
-1.093797812399983

> 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.

I hope to verify whether vmd really ignore the ATOM Index column and whether

this problem is from the kernel code of vmd or just the lammpstrj plugin. So
I disorder the ATOM index.
It's likely that it did. See the coords of ATOM 2 and ATOM 3, they exchanged
to each other.
THIS IS JUST A TEST.

> 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.
>
>
Yes. ATOM data is disordered, but ATOM indexes are still stored in dump
file,
say, in the top lammpstrj file, ATOM Index 23 is output in the first line of
these data,
but the index number is same in all frames. So I hope The index of this atom
will be
indexed to 23, not 1. Is there any way to fix it ?

Thank you!

Cun Zhang

> 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.
> 

-- 
Blog: http://www.edwardpku.com/cun