From: 王妙郡 (
Date: Fri Apr 22 2016 - 09:34:46 CDT

Dear users,

Thank you Axel.
My vmd version is 1.9.2 and my topotool version is 1.5. I output dcd file
from lammps and read the file in vmd by psf and dcd. After visualize and
changing atom types in vmd, I output my file using topo writedatafile in
order to read in lammps.
>From Axel recent answer, a question rises out of my mind that when I am
reading water molecules also using dcd and psf file in vmd, does vmd read
my bonds correctly? I see the label of water molecule in vmd, two H and one
O have the same residue, but will the output data of bonds by using "topo
writelammpsdata" be correct?
Thank you!

On Tue, Apr 19, 2016 at 4:38 PM, Axel Kohlmeyer <> wrote:

> On Tue, Apr 19, 2016 at 4:05 PM, 王妙郡 <> wrote:
>> Dear users,
>> I attend a problem while writing out the data file from VMD. I have 4
>> bond types and 5 angle types during simulation; however, when I try to
>> output my data using "topo writedatafile" from VMD, the data file shows
>> that I only have 1 bond type and 1 angle type. I think that write_data
>> command in LAMMPS can solve this problem, but I am curious why this is
>> happening in VMD . Also, is there any way to solve this problem by using
>> VMD?
> from your description ​it is not clear which files in which formats you
> are read​ing into VMD and what you do in between. also, it is crucially
> important that you let us know which version of VMD exactly and
> particularly which version of the topotools plugin you are using. if you
> are not using the latest version of each, you may be missing features or
> there may be bugs that have been corrected since.
> that said, topotools can only output information that is present in VMD.
> most trajectory file formats do not provide topology information and also
> some topology file format, e.g. psf do not contain any type information
> outside of atom types. so unless you are using a suitable process of
> reading the complete information or reconstructing it from available
> information (which may or may not produce the exact same result, as
> different tools may have differences in their heuristics and assumptions
> about topologies), topotools will write out incomplete data. topotools was
> deliberately designed to be agnostic to force fields and thus any
> information not present cannot be automatically recovered.
> axel.
>> Thank you.
>> Miao-Chun
> --
> Dr. Axel Kohlmeyer
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.