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