VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 29 2015 - 06:45:34 CST
a few comments:
- you are using an outdated version of topotools (1.2, current is 1.5)
with known bugs. the easiest way to update is to replace your VMD
version with the latest version 1.9.2
- your description doesn't make sense, or your leaving things out that
you did. guessangles depends on the bond topology to construct the
angles, yet you don't seem to have C-C bonds in your file. so it is
not clear to me, where the angles should come from. if you managed to
get rid of the bonds manually, e.g. with a text editor, you can, of
course, do the same on the angles. the file format for data files is
well documented in the LAMMPS manual.
- you should be able to avoid creating angles between any atom
containing carbons, by using the -sel flag to restrict the atoms to be
considered with a selection. if it doesn't work, please report it as a
bug and provide the means to reproduce it.
- you can simply use the getanglelist command and then process the
returned list to remove the angles you don't want. the updated list
can be reassigned via setanglelist. of course, this requires
sufficient proficiency of Tcl scripting.
On Thu, Jan 29, 2015 at 12:09 AM, Majid Shahbabaei
> Dear VMD USERS,
> I did make a model that consists of a box (SPC/E water molecules inside a
> two carbon atom walls ) connected to a carbon tube. I used the "topotools"
> to convert my PDB data to LAMMPS and also I have used the "topo guessangles"
> command to show the angles. Please take a look at the data file obtained by
> topotools which added in the end of this email. I just want to consider
> H-O-H angles and neglect the C-C-C angles.
> Could anybody tell me how to delete the C-C-C angles through VMD?
> LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools
> v1.2 on Tue Jan 27 11:10:34 KST 2015
> 3372 atoms
> 4467 bonds
> 28243 angles
> 0 dihedrals
> 0 impropers
> 3 atom types
> 1 bond types
> 2 angle types
> 0 dihedral types
> 0 improper types
> # Pair Coeffs
> # 1 C
> # 2 HW
> # 3 OW
> # Bond Coeffs
> # 1
> # Angle Coeffs
> # 1 H-O-H
> # 2 C-C-C # I want to delete that
> 1 12.011000 # C
> 2 1.008000 # HW
> 3 15.999000 # OW
> Thanks in advance
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.