Questions tagged [vmd]

Questions about the VMD software.

Filter by
Sorted by
Tagged with
8
votes
2answers
153 views

File type to write bond information

I have an xyz file upon which after processing in Python, I determine bonds between different atoms. What would be the correct file type that I can write to visualize this bond information in VMD?
10
votes
2answers
189 views

How to include individual PBC box dimensions in xyz file format compatible with VMD

I am using ASE to write an xyz file. Each frame in the file has a different PBC (periodic boundary condition). Currently, a frame starts like this: ...
11
votes
2answers
174 views

Recalculate atom positions to account for periodic boundary conditions

I have the output of a simulation done using Periodic boundary conditions (PBC), however, the atom positions have been resolved, i.e. there are atoms outside the PBC-box now. Is there a software/...
11
votes
1answer
115 views

Calculating RMSF in VMD

As a part of my coursework I have to calculate root mean square of fluctuation (RMSF) of a protein trajectory over the last 5 nanoseconds of simulation. I have used the inbuilt ...