Dear lammps users,
I have simulated a protein in lammps. I am using the dcd file 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 name of the protein(, and also the name of each molecule which is needed for secondary structure). Is there any alternative? As I have simulated the protein in lammps and now I can not plot the secondary structure.
kind regards,
That has nothing to do with LAMMPS. dcd files do not contain any of that information. they only contain coordinates.
…and LAMMPS doesn’t require any of that information to do simulations either.
You have to load some other file into VMD first that provides that information to VMD. Head over to the VMD mailing list and search the archives there are plenty of discussions on that.
In the VMD “world” people usually use a .psf file in combination to provide the required data.