Pulling

Introduction

Here, we will discuss how to pull various moulecules. As an example, I will take 10w.xyz file and 1cl.xyz file to construct chloride anion above water cluster:

JKMD 10w.xyz -recenter 1cl.xyz -chrg -1 -moveto [6,0,0] -ns 0 -loc

This will take quite short time as only single-point calculation is performed. In the end you will get this:

filesstructure

This is the system we will work with.

Pulling a specie

If you want to pull the chloride, it is quite easy because it is a separate file, i.e. a separate specie. Let us pull it towards the cluster:

JKMD 10w.xyz -recenter 1cl.xyz -chrg -1 -moveto [6,0,0] -EF_c_COM [-1,0,0] -ns 1000 -loc

The force applied on the COM = center of mass is 1 kcal/mol/Angstrom in the direction of the cluster.

We could also go oppositely and pull the water cluster towards the chloride. By applying 1 kcal/mol/Angstrom on the cluster COM, the force gets redistributed over the cluster atoms to give all species the same acceleration.

JKMD 10w.xyz -recenter -EF_c_COM [1,0,0] 1cl.xyz -chrg -1 -moveto [6,0,0] -ns 1000 -loc

Pulling a fragment

Well I have not built this yet. However, at some point I will. For now you can just simply split your xyz file into fragments on your own.