From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Feb 16 2020 - 17:47:25 CST

You are looking at the webpage and run the commands without thinking, which
is always a bad idea. The point of the example is to show you the process,
not to give you a sequence of commands that will always work. there are
just too many situations for different applications, where you have to use
a modified version of the commands.

VMD doesn't care what kind of a system you have. all it "knows" is that
there are positions and those have properties like names, types, bonds, and
so on attached to it. The TopoTools plugin in particular was conceived to
allow scripting of all kinds of topology manipulation operations regardless
of the kind of system in question, which makes it different from many other
tools, that do make some more assumptions about the system (and thus are
less flexible). but with the added flexibility comes the price that you
have to consider more carefully what you are doing. TANSTAAFL!

I don't have the time (and patience) to play 20 questions with you to
figure out what exactly is your situation and are your specific needs and
then present you with a custom tailored set of commands for you. rather the
way to go about it is that you look at each line and understand what it
does (e.g. by comparing it to the VMD script command documentation or a Tcl
script documentation/tutorial). once you understand the purpose, you can
easily adjust and modify the command to what suits your specific situation.
as a scientist you should be used to this procedure as this is what you
need to do for almost anything since there are rarely cases where you can
blindly follow a given sequence of instructions without thinking.
otherwise, this wouldn't be science but an assembly line factory job.

Axel.

On Sat, Feb 15, 2020 at 6:14 PM Amir Afshar <amir.afshar3_at_gmail.com> wrote:

> Dear Axel,
>
> I went through the instructions given by you in that link for detection
> and removal of overlapped atoms in VMD. It seems it only applies for
> biological structures with extension of "PDB" or "PSF". I have two Lammps
> data files for merging and it doesn't accept the extension of data file I
> want to load through " set solute [mol new solute.psf waitfor all]"; It
> says, "Could not determine file type for file '......' from its extension,
> when I loaded into my VMD TkCosole. May you please let me know how it works
> for non-biological structures to build a data file of two merged structures
> with no atom overlapping?
>
> Thank you very much.
>
> Best,
> Amir
>
> On Sat, Feb 15, 2020 at 11:10 AM Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
>
>>
>> https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks#TOC-Combine-multiple-data-files-with-overlap-detection-and-removal
>>
>> On Sat, Feb 15, 2020 at 11:53 AM Amir Afshar <amir.afshar3_at_gmail.com>
>> wrote:
>>
>>> Dear Axel,
>>>
>>> I have built a setup simulation of water confined by graphene sheets.
>>> For this, I used the "mergemols" in "topotools" option in VMD. Would you
>>> please let me know how I can check and remove if there is any overlap
>>> between the atoms in my merged data file?
>>>
>>> I used the Nanotube builder in VMD and generated graphene sheets, then I
>>> added the water box through "topo readlammpsdata" option then merged two
>>> structures.
>>>
>>> Thank you very much.
>>>
>>> Regards
>>> --
>>> Regards,
>>> Amir Afshar
>>>
>>>
>>
>> --
>> 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.
>>
>

-- 
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.