VMD-L Mailing List

From: Rakesh K (rakeshkrish_at_iitb.ac.in)
Date: Tue Nov 24 2020 - 12:22:26 CST

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.*