topo and data file generation!!!

Dear all,

I am new LAMMPS user and currently trying to learn it.

I have a very simple question. Can anyone please suggest me how to create a LAMMPS data file from a xyz or pdb file? Here is the xyz file attached for TIPS3 water model.

For info, I used the topo plugin from VMD using the command topo writelammpsdata data.mysystem molecular. I am using the LAMMPS on windows. The VMD topo plugin on Windows did not produce any output file, so I used the VMD on Mac, and created the following data file. But I have not found any mention of charges. Also how to add the bond parameters, angle coefficients etc in data file? Shall I have to do it by hand?

Thank you,

Tim

data.mysystem (156 KB)

SPCE_water.xyz (152 KB)

Hi Tim

http://lammps.sandia.gov/prepost.html

(Also check http://sourceforge.net/projects/moleculardynami/)

Some tools can generate force-field information and charges for your
molecules. Other tools let you add this later by hand. Some tools
can build a nanotube, or a protein chain, and solvate a complex
molecule. Others can not.

If you plan to simulate a complex molecular system, it might be easier
to build it using the more specific tools which come with other MD
codes, and then convert the resulting files to LAMMPS data/in format
using these codes:
http://lammps.sandia.gov/doc/Section_tools.html
Unfortunately these tools may have bugs and not maintained.

Jason Jambert and I have attempted to add the ability to lookup
force-field parameters for AMBER-GAFF and OPLS-AA into moltemplate
(v1.18). (SPCE and TIP3P are present as well.) However these
features are not yet thoroughly tested (or even well documented). As
with all tools, use with caution and be ready to check the results.

Cheers
Andrew

Dear all,

I am new LAMMPS user and currently trying to learn it.

I have a very simple question. Can anyone please suggest me how to create a
LAMMPS data file from a xyz or pdb file? Here is the xyz file attached for
TIPS3 water model.

For info, I used the topo plugin from VMD using the command topo
writelammpsdata data.mysystem molecular. I am using the LAMMPS on windows.
The VMD topo plugin on Windows did not produce any output file, so I used
the VMD on Mac, and created the following data file. But I have not found
any mention of charges. Also how to add the bond parameters, angle
coefficients etc in data file? Shall I have to do it by hand?

tim,

this is the typical thing that happens, if you throw away the manual
with the wrapping. while you may get away with it, when you get
yourself a new iphone, with a new MD code and visualization software
(and scientific software in general), this is a bad idea and a recipe
for trouble.

here are few reminders and suggestions:
- the topotools plugin is not a complete, automatic,
just-stuff-some-coordinates-in-here-and-you-get-what-you-want tool. it
is meant to help building topology files and mean to simplify the
complex and error prone parts of that process. you still have to write
a script and there are some detailed examples on its home page that
show the principles.
- VMD on windows has some well known and well documented quirks. one
of them is that its current working directory (when launched from the
desktop) is the installation directory, which is usually not writable
(on a decently managed fairly recent windows machine). all you have to
do is to first change into a directory where you have write
permissions and it works fine. taking the path through using a mac is
an extreme hack.
- of course there are no charges assigned? how should VMD know that
you intent to model TIP3P and not SPC or SPC/E or TIP4P or ST2 or one
of the gazillion other water potentials. to the best of my knowledge,
software that has mind reading abilities has not yet been invented.
furthermore, you also need to check that you have the correct topology
information (VMD is primarily a visualization tool and thus doesn't
care about anything but atoms and bonds). thus topotools can only
write out, what you input.
- there is no way to store force field information into VMD in a
consistent fashion, thus topotools doesn't attempt to do it. and if
you had spend some more time reading the LAMMPS documentation, and
checked out the existing examples and tutorials more thoroughly, you
would have seen, that you don't *have* to put those force field
parameters there, you can also put them into your input file (or use
and include file). personally, i very much prefer that over the data
file, because that makes is much more visible, consistent and
explicit; all of that is helpful for good simulations, because you
*want* to know what is going on and not just hope that the software
will somehow sort it out for you. most software that promises that,
does a pretty bad job and you don't want sloppy simulation results, or
do you?

in general, while the LAMMPS manual has an extensive "howto" section
and lots of examples. i suggest that rather than immediately digging
into your specific research project, you start by going over this
material and figure out what and how it works and how you can modify
those and what kind of impact such modifications have. so please take
a few steps back, have a second, more careful look, and don't rush
things.

axel.