VMD-L Mailing List

From: Aric Newton (agnewton_at_berkeley.edu)
Date: Thu Feb 16 2012 - 10:27:38 CST

Axel,

I originally built the model in Materials Studio. I exported it as a
*.car/ *.mdf file pair; made a LAMMPS data file with the msi2lmp tool;
ran the simulation; and wrote an unscaled trajectory in the LAMMPS
(*.atom) format and an unwrapped trajectory in the GROMACS (*.xtc)
format.

I generated a *.psf from the lammps datafile and loaded the trajectories
(a different model for both trajectory formats). I can see the H-bonds
via the Graphical Representation> Hbonds and generate the data files and
a multiplot graph with the Analysis>Hydrogen Bonds extension. I do
still receive the "Warning) multiplot: Data vector empty, ignoring
plot!" message. I accept it as a warning not an error.

I assume that the tool is functioning as it should (input parameters at
the end). What I would like to ask is if either of the H-bonds methods
is calculating H-bonds across the periodic boundaries? I ask because
the anion starts in the center and during the trajectory migrates toward
the cell boundary. The output indicates that as the trajectory
progresses, the number of H-bonds decreases when the anion is near the
periodic boundary. The graphs of the H-bonds v. frames for the wrapped
and unwrapped trajectories are not equivalent, but the decrease in the
number of bonds is present in both (i.e. unwrapped atoms can't H-bond,
wrapped atoms can H-bond, but H-bonds can't cross the cell boundary).
Visually, the trajectory appears to confirm this (no H-bond
representations cross the boundary). Is this an artifact of the way that
I have loaded the trajectory or something the tool doesn't do?

Thank you,

Aric

Parameters used in the calculation of hydrogen bonds:
- Atomselection 1: resid 407
- Atomselection 2: not resid 407
- Update selections every frame: yes
- Initial frame: 0
- Frame step: 1
- Final frame: 5000
- Donor-Acceptor distance: 3.0
- Angle cutoff: 20
- Type: none
- Write a file with H bond/frame data: yes
- Filename: ohz_wrap_hbonds.dat

Printing frame/hbond data to file... Done.
Warning) multiplot: Data vector empty, ignoring plot!

 

On Wed, 2012-02-15 at 19:14 -0500, Axel Kohlmeyer wrote:
> On Wed, Feb 15, 2012 at 7:11 PM, Aric Newton <agnewton_at_berkeley.edu> wrote:
> > Dear John and Axel,
> >
> > Thank you for your replies and the more detailed info on how the Hbond
> > algorithm does what it does. The naming conventions appear to be key.
> > Your tips also suggest I should revisit topotools docs as the guessatoms
> > options have been expanded since my last reading.
> >
> > I can render the Hbonds through the Graphical Representations dialog but
> > haven't had luck (yet) with the Analysis> Hydrogen Bonds extension. 5
> > minutes after I hit <send> I realized that I have the data file in other
> > formats (*.car/ *.mdf) and can convert it to a *.pdb file. I'll use
> > that as a starting point and keep at it.
>
> aric,
>
> it'll be better to generate a .psf file instead of .pdb file
> since the .psf doesn't contain coordinates, but the .pdb does.
> you usually don't want those "parasitic" coordinates in
> your analysis, right?
>
> cheers,
> axel.
>
>
> >
> > Thanks again to you both.
> >
> > Aric
> >
> >
> > On Wed, 2012-02-15 at 10:13 -0600, John Stone wrote:
> >> Hi,
> >> I thought I'd chime in and amplify Axel's comment regarding atom
> >> names/types. The hbond visualization and analysis functions of VMD
> >> look for atom names/types that they recognize, if you're using
> >> a naming scheme that VMD doesn't understand, then it won't be able to
> >> do the visualization/analysis you want. The simplest way to fix this
> >> is to rename the atoms, and then do a "mol reanalyze" so VMD re-tags
> >> the atoms it is able to recognize.
> >>
> >> Cheers,
> >> John Stone
> >> vmd_at_ks.uiuc.edu
> >>
> >> On Tue, Feb 14, 2012 at 04:36:13PM -0500, Axel Kohlmeyer wrote:
> >> > dear aric,
> >> >
> >> > On Tue, Feb 14, 2012 at 3:22 PM, Aric Newton <agnewton_at_berkeley.edu> wrote:
> >> > > Dear VMD users,
> >> > >
> >> > > I am trying to use the Hydrogen Bonds extension to assess the hydrogen
> >> > > bonding of a hydroxyl anion in SPC/E water. I have run the simulation
> >> > > in LAMMPS and am loading it into VMD using the sequence 1) topotools
> >> > > readlammpsdata <file>; 2) topo guessatom element mass; and 3) loading
> >> > > the lammps trajectory (*.atom format) into the molecule.
> >> >
> >> > better yet. try:
> >> >
> >> > topo guessatom lammps data
> >> >
> >> > to import/reconstruct as much VMD information from the
> >> > LAMMPS data file as possible. that should set atom names
> >> > as well.
> >> >
> >> >
> >> > > The Hydrogen Bonds extension executes with what appears to be valid
> >> > > input data, but returns a "Warning) multiplot: Data vector empty,
> >> > > ignoring plot!" Obviously, the output is not reliable. However, there
> >> > > is no overlap in atom selections. Each water molecule has a unique
> >> > > resid but they all have the same molecule id: 0 and chain: X. I have
> >> > > provided the Hydrogen Bonding scripts parameters from the Terminal
> >> > > window below and the output from a TkConsole command line attempt as
> >> > > well. I've looked through the archive to try to see if there is
> >> > > something obvious I am missing, but I have yet to locate it.
> >> > >
> >> > > I have used the brH.pdb file in the /protein directory distributed with
> >> > > VMD to test if the problem is user-error or something else. The
> >> > > Graphical Representations> Drawing Method> Hbonds technique depicts
> >> > > H-bonds in the brH.pdb model. Although,the TkConsole indicates that
> >> > > there are 441 hbonds found and provides a list when I use the Hydrogen
> >> > > Bonds Extension, the "Warning) muliplot: Data vector empty, ignoring
> >> > > plot!" message persists and no graph is generated.
> >> > >
> >> > > I've tried this with both v.1.9 and the new v.1.9.1 of VMD on Ubuntu
> >> > > 10.04 LTS and v.1.9 on Mac OS X 10.7. Are hydrogen bonds absent because
> >> > > there are no "explicit" hydrogen atoms in the structure? The "topo
> >> > > guessatom element mass" correctly assigns the elements and I can color
> >> > > the model (correctly) by element. But there is no indication what the
> >> > > element is when I pick the atoms in the Display (names=types). Where is
> >> > > this info stored and how can I get the Hbonds tools to see it?
> >> >
> >> > each atom has various properties (name, type, element, mass, charge,
> >> > x, y, z, resid, residue, resname, fragment, index, serial, ...).
> >> > those are stored with the molecule topology information.
> >> >
> >> > this can be accessed from script level with atom selections.
> >> > e.g. to give all atoms of type 1 the name "OW" you would do
> >> >
> >> > set sel [atomselect top {type 1}]
> >> > $sel set name OW
> >> > $sel delete
> >> >
> >> > and so on. the hbond plugin assumes a combination of
> >> > PDB/NAMD/CHARMM/Amber naming conventions to
> >> > identify hydrogens, and hbond donors and acceptors.
> >> > this may not be 100% consistent with the Hbond representation.
> >> >
> >> > so if, using the more extended: topo guessatoms lammps data
> >> > doesn't help to get you up to speed, you can just write a little
> >> > script that renames the atoms by lammps type number to something
> >> > that will be properly recognized by VMD and then write it
> >> > out as a .psf file for later re-use.
> >> >
> >> > due to the way, how lammps strips of all information about
> >> > conventional naming from its input, you have to resolve to
> >> > these tricks. to do analysis.
> >> >
> >> > life is tough. :-(
> >> >
> >> > cheers,
> >> > axel.
> >> >
> >> >
> >> > >
> >> > >
> >> > >
> >> > > Sorry if I have overloaded you with diagnostic info but I am stumped.
> >> > > Thank you for reading.
> >> > >
> >> > > Sincerely,
> >> > >
> >> > > Aric
> >> > >
> >> > >
> >> > >
> >> > > Parameters used in the calculation of hydrogen bonds:
> >> > > - Atomselection 1: type 3 4
> >> > > - Atomselection 2: type 1 2
> >> > > - Update selections every frame: yes
> >> > > - Initial frame: 0
> >> > > - Frame step: 1
> >> > > - Final frame: 5001
> >> > > - Donor-Acceptor distance: 3.0
> >> > > - Angle cutoff: 20
> >> > > - Type: none
> >> > > - Write a file with H bond/frame data: no
> >> > >
> >> > >
> >> > > Found 0 hbonds.
> >> > > donor acceptor occupancy
> >> > > Warning) multiplot: Data vector empty, ignoring plot!
> >> > >
> >> > > Alternate TkConsole output type 1 and type 2 are O(water) and H(water),
> >> > > respectively.
> >> > > Main console display active (Tcl8.5.6 / Tk8.5.6)
> >> > > (NPT_iso500ps) 1 % set sel1 [atomselect top "type 1"]
> >> > > atomselect20
> >> > >>Main< (NPT_iso500ps) 2 % set sel2 [atomselect top "type 2"]
> >> > > atomselect21
> >> > >>Main< (NPT_iso500ps) 3 % measure hbonds 3.5 20 $sel2 $sel1
> >> > > {} {} {}
> >> > >>Main< (NPT_iso500ps) 4 %
> >> > >
> >> > >
> >> > >
> >> > >
> >> >
> >> >
> >> >
> >> > --
> >> > Dr. Axel Kohlmeyer
> >> > akohlmey_at_gmail.com http://goo.gl/1wk0
> >> >
> >> > College of Science and Technology
> >> > Temple University, Philadelphia PA, USA.
> >>
> >
> >
>
>
>