VMD-L Mailing List

From: Yann Claveau (yann.claveau_at_univ-rennes1.fr)
Date: Tue Jul 13 2021 - 08:19:38 CDT

Hi all,

I want to unwrap lammps trajectories. I opened the dump.lammpstrj in
vmd, then did

pbc unwrap -all

It worked. Then I saved the new coordinates. When opening the new file,
all types have been renamed.

for instance in the dump.wrapped.lammpstrj : 0 = 1, H =2, Si = 3

while in the dump.unwrapped.lammpstrj : Si = 1, O = 2, H = 3.

The problem is that I use MDAnalysis that needs the *.data file too. It
would be troublesome if the types in the data file are not the same as
in the dump.

Is there a way to force vmd to keep the same atom types when saving the
new coordinates ?

Thanks, 

-- 
Yann claveau, PhD
Département Matériaux-Nanosciences
Bât. 11A, bureau 122,
Campus de Beaulieu
Institut de Physique de Rennes - UMR-CNRS 6251
Université de Rennes 1
35042 Rennes cedex FRANCE