Problem with LAMMPS dump molfile

Dear Axel,
Thank you for the information.
All of VMD plugins were copied to the same directory of the simulation inputs and I removed the path, but the problem persists.
I am indeed using lammps 64-bit on windows 64-bit. However, I noticed that VMD is 32-bit. Could that be the problem?
Is this plugin the only way to build the trajectory files with xyz or pdb extensions? I can use Avogadro or Ovito to read common lammps dump files, but they do not provide easy ways to observe the molecules/bonds formations/breakings, so that is why I am trying to use the molfile plugin. Do you have any reccomendation on that?
Thank you so much.

Rene


> Dear Dr. Kohlmeyer,
>

​in the future, please post questions about LAMMPS to the lammps-users
mailing list and not to me directly​. the mailing list is archived, so that
other people with similar problems can research the existing solutions and
recommendations. thanks for your understanding.

>
> I am having some problems in using the dump molfile command in LAMMPS, as
> it states the following error: "Error on proc 0: No suitable molfile plugin
> found (../dump_molfile.cpp:105)"
> In some websites I have seen a couple of people with the same problem,
> which is that lammps is unable to find the plugins. I am using lammps for
> windows, but when I specify the directory with VMD plugins, it just doesn't
> work. Could you please advise me on that?
>
> This is the dump command I am using:
>
> ​dump 4 all molfile 25 hmx*.pdb pdb .C:\Program Files (x86)\University of
> Illinois\VMD\plugins\WIN32\molfile\
>

​there are two problems:
1) there is a '.' character ​in front of the "C:" drive letter, which would
make it an illegal path.
2) your pathname has blanks in it. LAMMPS will thus not recognize it as one
argument, but as multiple. even with the corrected drive letter, it would
look in "C:\Program", which is - obviously - not a valid path. you have to
use single or double quotes around the path.

an easier remedy for this is to copy the desired molfile plugin into the
working directory and not specify a path at all.

it looks like you are on a 64-bit windows installation. did you install a
32-bit LAMMPS binary or a 64-bit one? please note, that the 64-bit binary
cannot load 32-bit windows plugins.

axel.
​

Dear Axel,
Thank you for the information.
All of VMD plugins were copied to the same directory of the simulation
inputs and I removed the path, but the problem persists.
I am indeed using lammps 64-bit on windows 64-bit. However, I noticed that
VMD is 32-bit. Could that be the problem?

​yes, those are not compatible. you can only open and use 32-bit windows
plugins from a 32-bit windows binary.​

Is this plugin the only way to build the trajectory files with xyz or pdb
extensions? I can use Avogadro or Ovito to read common lammps dump files,
but

​.xyz files can be natively produced in LAMMPS with the xyz dump style.
neither .xyz nor .pdb are good choices, you lose a lot of precision in .pdb
and .xyz files carry only a minimal amount of information.

they do not provide easy ways to observe the molecules/bonds
formations/breakings, so that is why I am trying to use the molfile plugin.
Do you have any reccomendation on that?

​i use VMD, which can read native LAMMPS trajectories (custom or atom) in
text format and VMD has a "dynamic bonds" representation, that can model
bonding processes in many cases well, especially when assigning and writing
out element labels in dump style custom and setting them via dump_modify​

​axel.​