LAMMPS

It is very important to visualize molecular dynamics (MD) trajectories since there are many aspects of MD simulations which are difficult to identify without a proper visualization tool. Improper bounday condition in MD is one of such examples. I use Visual Molecular Dynamics (VMD) to visualize my MD simulations. Some of my movies, created using VMD, are shown below.

In appendix A of my PhD thesis, I share a MATLAB code to get coordinates of carbon atoms in a graphene sheet. The code also generates the data file required for LAMMPS. In addition, I included a sample input and the corresponding output files from LAMMPS. I hope this will be useful for those who would like to learn MD simulations.

Visual Molecular Dynamics (VMD) package can also be used to obtain coordinates of graphene.

 A postdoctoral position with primary focus on molecular dynamics simulations is available immediately at Shenoy Research Group  under the direction of Prof. Vivek B. Shenoy .  We are looking for a strongly motivated candidate to work on modeling of nanomaterials and soft materials. The ideal candidate will have a background in materials science/computational physics with expertise in molecular dynamics simulations with LAMMPS or other packages.  This individual will have the opportunity to be directly involved in complimentary experimental investigations, both at Penn and our collaborators in industry. 

The National Nanotechnology Infrastructure Network’s computational project (NNIN/C) is a multi-university initiative, funded by the National Science Foundation (NSF) as part of NNIN, to establish a user accessible national computing resource for nanotechnology. This network is open to the academic and industrial research community and provides hardware resources and simulation tools dedicated to nanoscience
research.

 
FOR BEGINNERS :::::  I have uploaded Problems & Solutions in Molecular Simulations in Mechanics and Physics ( with Matlab Code & LAMMPS Script) .

CLICK HERE TO DOWNLOAD 

A postdoctoral position is available at the Mechanical Engineering Department of the University of Connecticut in the area of coarse-grain molecular dynamics simulation of cellular membranes and filaments. Extensive experience in molecular dynamics simulation of soft materials and parallel coding is required. Experience in the use of force fields and LAMMPS is highly desirable.