VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sat Feb 15 2020 - 14:57:49 CST

I was actually unaware that Axel already had an example input, and he
posted a link to it for you.

On Sat, Feb 15, 2020 at 2:32 PM Amir Afshar <amir.afshar3_at_gmail.com> wrote:

> Hi Giacomo,
>
> Thank you for your note. May you please let me know how I can pass a
> custom selection to the "topo" command in VMD to tell it to only save a
> data file that consists only non-overlapping atom?
>
> Thank you very much.
>
> Best,
> Amir
>
> On Sat, Feb 15, 2020 at 11:15 AM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hello Amir, you can probably take inspiration from the many scripts in
>> the VMD website used to set up protein simulations. In those, selections
>> of overlapping atoms are used to instruct the psfgen program to delete the
>> corresponding atoms from the system being prepared.
>>
>> You probably won't use psfgen for a LAMMPS data file, but you should be
>> able to pass a custom selection to the "topo" command to tell it to save a
>> data file that contains only non-overlapping atoms.
>>
>> Giacomo
>>
>> On Sat, Feb 15, 2020 at 11:54 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
>>>
>>>
>>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Research collaborator, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>
>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin