I model 194 water molecules with the flexible SPC model (harmonic bond and harmonic angle). Through VMD, I notice that there’s a bond automatically formed between each two H atoms of a water molecule. I don’t know why because I’m sure I didn’t mention those H-H bonds in my data file.
Does someone know why?
I model 194 water molecules with the flexible SPC model (harmonic bond and
harmonic angle). Through VMD, I notice that there's a bond automatically
formed between each two H atoms of a water molecule. I don't know why
because I'm sure I didn't mention those H-H bonds in my data file.
Does someone know why?
there is not information here. what kind of file(s) do you load into
VMD and does it/they contain sufficient information so that VMD can
recognize the bond topology and elements as you are simulating?
VMD will try to guess information it needs and the less appropriate
information it gets the more likely it is that it will guess wrong.
1) What kind of file are you reading in VMD?
Many files do not contain bond topology information, (PDB files and
XYZ files, etc). In that case, VMD will attempt to draw bonds between
pairs of compatible atoms which are close to eachother. If it can not
identify the atom type, then it will do this by default. To avoid
that, you must be careful to use atom-names which VMD recognizes.
For example, if you want VMD to read a PDB file containing water
molecules, then it needs to recognize the atom-names and residue type
for water. (I've attached a PDB file "water_pdb_file_example.pdb" in
a format that VMD can understand. I also attached a picture. VMD
does not draw bonds between the "H1" and "H2" atoms.)
However if you are reading a LAMMPS data file that you have already
created (using "topo readlammpsdata"), then the only bonds that you
see should be the bonds that appear in the "Bonds" section of your
data file. If you are seeing bonds between the hydrogen atoms in that
case, then you have a problem in your DATA file.
2) (my apologies for the solicitation)
I myself keep hearing about a flexible SPC water model, but I'm not
sure exactly which paper it refers to. I assume this model is based
on the work of Toukan and Rahman, Phys. Rev. B 31, 2643 (1985)
...however the wiki article mentions several different papers:
In any case, if you are able to prepare LAMMPS input files for the
flexible SPC water molecule, I would love to post it as a moltemplate
example. Are you willing to share it?
water_pdb_file_example.pdb (60.2 KB)