VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 26 2021 - 00:37:41 CST

I think there were other recent inquiries about PBC wrapping
and/or rewrapping of LAMMPS trajectories on VMD-L, I'd suggest
searching the list for these recent postings. I think it came
up sometime just in the last half year or so if I'm not mistaken.
I'm not a LAMMPS expert, so I can't provide any specific guidance.

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 14, 2021 at 06:11:38PM +0530, Rakesh K wrote:
> Hi all,
>
> I have simulated polymer system with attractive and repulsive LJ using PBC
> conditions in LAMMPS. I wanted to wrap the simulation in the periodic box
> in VMD. I used the following command.
>
> pbc wrap -center com -centersel "residue 1" -compound res -all
>
> Different residues and types were used in centersel and wrapped, but the
> resulting trajectory will have fluctuating positions of polymers from one
> side of the box to another side.
> This looks bad if all the polymers are of one cluster and they split for
> some time due to packing.
>
> Is there any set of commands or ways to wrap the system such that the
> system wraps correctly?
>
> Thanks and Regards,
> Rakesh K.
> Research Scholar,
> IIT Bombay. 

-- 
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