VMD-L Mailing List

From: Amir Afshar (amir.afshar3_at_gmail.com)
Date: Sat Feb 15 2020 - 13:31:55 CST

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
>