Messages

1

General Questions and Answers / Re: How to see the trajectory of the atoms after a relaxation

« on: July 9, 2012, 21:51 »

The trajectory file (trajectory.nc) that is generated in MolecularDynamics doesn’t work. However, the trajectory file that is generated in OptimizeGeometry works.

Attached is the generated trajectory file that I can not read.

Thanks in advance.

2

General Questions and Answers / How can I do periodic boundary conditions?

« on: July 6, 2012, 01:25 »

I would like to build a finite graphene sheet with periodic boundary conditions in both directions (i.e. in y and z axes) to study the stability of defects in graphene at finite temperature. How can I do this?

3

General Questions and Answers / How to see the trajectory of the atoms after a relaxation

« on: July 6, 2012, 01:08 »

I did a molecular dynamic simulation with graphene, and I would like to see the trajectory of the atoms. So I clicked the option save trajectory in Molecular Dynamics, and a file was generated (i.e. trajectory.nc) but I don’t know how to read it, to make a video or just to know the position of the atoms after the relaxation.