From: Runak R (
Date: Mon Sep 13 2021 - 11:36:43 CDT

Dear VMD users,

I have simulated a protein in LAMMPS. I am using the dcd file format as the
output to plot the secondary structure in VMD. I got the segmentation
error in VMD.

I found that LAMMPS dcd output does not include the name of each segment of
the protein (,and also the name of each molecule which is needed for
secondary structure). Is there any alternative? If I can extract just the
atomic properties (such as mass, atom type, atom ID, atom coordinates), not
the residue properties, can I use the initial psf file of the protein that
contains residue properties to create a trajectory file suitable for
secondary structure? (using automatic psf builder) If no, is there any
analysis that I can do with the protein alternatively?

kind regards,