VMD-L Mailing List

From: SHIVAM TIWARI (t.shivam_at_iitg.ac.in)
Date: Thu Jan 04 2024 - 02:26:56 CST

Thanks axel, the first method looks clean, will try that. Thanks again.

Regards
Shivam

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________________________________
From: Axel Kohlmeyer <akohlmey_at_gmail.com>
Sent: Thursday, January 4, 2024 12:28:48 AM
To: SHIVAM TIWARI <t.shivam_at_iitg.ac.in>
Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: assigning segment id or a unique identity in lammps data file

You could use ::TopoTools::replicatemol with a 2 1 1 count to create a double size system replicated in x (or with other counts as desired).

Alternatively, you can apply the "move by" command to one of the two systems *before* merging.
If your original system has been created with periodic boundary conditions, then probably the first one will be more suitable, since for the second, you would likely need to manually adjust the box dimensions of the merged system.

Selecting on the index property should be safe though. The index property is guaranteed to be unique and assigned by VMD, not LAMMPS (so it is not the atom ID).

On Wed, Jan 3, 2024 at 1:07 PM SHIVAM TIWARI <t.shivam_at_iitg.ac.in<mailto:t.shivam_at_iitg.ac.in>> wrote:
Dear users,

I equilibrated a box of liquid with lammps and outputted the final configuration in the form of lammps data file. Now using this final configuration, I want to create another system, where I need two boxes of the same final configuration. So, I created the copy of the same data file. I merged these two datafiles using merge command of the topotools. Now since the coordinates of atoms in both the data file are same, the two boxes overlap in the merged data file, and I want to move one box away from the other by using "move by" command. However, I don't have any unique identity to be able to select one of the boxes . Although, I achieved it by selecting the atoms of one box based on the indices, I believe this approach is error prone.

I was wondering if there is a cleaner way to do this, for instance assigning a different segment id for each datafile. I tried doing this, but the "topo writelammpdata" command does not write segid to the data file. This can be done by writing out psf pdb files from the data file with "animate write" command and then assigning the segid. However, this approach also seems redundant. So, if anyone has an efficient way to do this?

regards,
SHIVAM 

--
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College of Science & Technology, Temple University, Philadelphia PA, USA