Re: [ESPResSo] pbc wrap

[Olaf Lenz]

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Hi!

The problem in your system is that the PDB files does not contain any
information other than the atom coordinates, an atom number, and an atom
type. There are no bonds, and also the residue or chain information is
not used.

Therefore it is not possible to learn anything about the system's
topology, for example which atoms belong to the same compound.
As long as this information is not available, "pbc join" can not do
anything useful, and also "-compound XXX" has no effect.
When you use "pbc wrap", this will simply mean that all atoms are
wrapped into the same unit cell, but VMD can not do anything about the
bonds, as it doesn't know about the bonds.

If you want to do anything about this, you will have to provide this
information in the PDB file. I don't know how to do this in ESPResSo
when the PDB format is used. I would recommend to use the VTF format for
output (writevsf and writevcf), where you have much more possibilities.

"pbc wrap -center com" can not do anything useful, as you do not give a
selection that the "center of mass" can refer to. Like this, it will
determine the center of mass of all atoms. If you want the unit cell to
be centered around a particular group of atoms, you have to specify this
group in the option "-centersel".

In principle, "pbc unwrap" should be of use, however the different
frames that you sent around recently are too far apart, so that single
atoms moved more than half a system box length. Accordingly, VMD can not
unwrap them, as it has no idea which direction the particle moved.
If you want to do anything about this, you will have to take snapshots
more frequently, or directly output the unwrapped coordinates, which is
probably the better solution anyway.


Olaf


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