Please add the following line to the beginning of the input file to start from scratch
start cluster
In other words, the top part of your input file should become
start cluster
echo
title "cluster"
memory total 2000 mb #I thought segmentation fault was due to some memory issues, so increase total from 400 to 2000mb.
geometry autosym
Pd -3.78493565 1.99241247 -0.78722757