Questions tagged [vmd]

Questions about the VMD software.

Filter by
Sorted by
Tagged with
6
votes
0answers
85 views

How to calculate radial distribution functions for MD trajectories without PBC, directly from coordinates with python?

I have been running MD simulations on water droplets with an ion in them. I am trying to implement a python program that could calculate the radial distribution function from ion to oxygen (or ion to ...
11
votes
2answers
349 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/...