Dear Jayanta,

The followings are a number of publications on MD simulation of pentacene molecule which may be helpful:

1-Molecular dynamics simulations of pentacene thin films: The effect of surface

on polymorph selection

Makoto Yoneya,*a Masahiro Kawasakib and Masahiko Andob

Received 24th May 2010, Accepted 30th June 2010

DOI: 10.1039/c0jm01577f

Molecular dynamics simulations were performed for multi-layer pentacene thin films using a simple

model surface. Two pentacene polymorphs, low-temperature (LT) and high-temperature (HT), were compared by examining their stability on a substrate and under free surface conditions. It was found that the LT polymorph was destabilised by the presence of substrate and free surface effects, which transformed the HT-polymorph over the course of our simulations. Suppression of the molecular

fluctuations along the long molecular axis by these surface effects was suggested as the source of this destabilisation.

http://pubs.rsc.org/en/content/articlepdf/2010/jm/c0jm01577f?page=search

2-Molecular dynamics simulation of pentacene diffusion. From Enhancing 2D growth of organic semiconductor thin films with macroporous structures via a small-molecule heterointerface

Boseok Kang, Moonjeong Jang, Yoonyoung Chung, Haena Kim, Sang Kyu Kwak, Joon Hak Oh & Kilwon Cho

Nature Communications 5, Article number: 4752 doi:10.1038/ncomms5752

http://www.nature.com/ncomms/2014/140826/ncomms5752/fig_tab/ncomms5752_F6.html

3-Molecular Dynamics Simulations for a Pentacene Monolayer on Amorphous Silica

Raffaele Guido Della Valle Prof.,

Elisabetta Venuti Dr.,

Aldo Brillante Prof.,

Alberto Girlando Prof.

First published: 6 May 2009Full publication history

DOI: 10.1002/cphc.200900084View/save citation

Molecular dynamics simulations are presented for “bulklike” and “filmlike” monolayers of pentacene deposited on a slab of amorphous silica. The two simulated systems, which mainly differ in the tilt angle between the pentacene molecules and the silica surface, exhibit structural and energetic properties that match the available measurements. The bulklike monolayer, the structure of which corresponds to that of the low-temperature polymorph of crystalline pentacene, is stable. The filmlike monolayer, in which the molecules are most closely normal to the surface, is instead thermodynamically metastable, in agreement with the experimental evidence.

http://onlinelibrary.wiley.com/doi/10.1002/cphc.200900084/abstract

4- Are Pentacene Monolayer and Thin-Film Polymorphs Really Substrate-Induced? A Molecular Dynamics Simulation Study

Makoto Yoneya*†, Masahiro Kawasaki‡, and Masahiko Ando‡

† Nanosystem Research Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono, Tsukuba 305-8568, Japan

‡ Hitachi Cambridge Laboratory, Hitachi Europe Ltd., J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom

J. Phys. Chem. C, 2012, 116 (1), pp 791–795

DOI: 10.1021/jp208468b

Publication Date (Web): December 02, 2011

Molecular dynamics simulations were performed for mono- and multilayer pentacene films on a simple model surface to study polymorphs of the deposition-processed thin-films. The layer-by-layer deposition history was taken into account by successive layer-stacking simulations of monolayer, bilayer and up to five-layered systems. We found that the tilt-free monolayer polymorph and the molecular tilting upon stacking layers on this monolayer were realized in the simulations even without any substrate interactions. These results imply that neither the monolayer nor the small angle tilted thin-film polymorph is substrate-induced as commonly explained. Our results also show a crucial dependence on the layer stacking history for the thin-film polymorph, which indicate that the thin-film polymorph would be induced with the layering history starting from the tilt-free monolayer.

http://pubs.acs.org/doi/abs/10.1021/jp208468b

5-Coupling between diffusion and orientation of pentacene molecules on an organic surface.

Paul Rotter, Barbara A. J. Lechner, Antonia Morherr, David M. Chisnall, David J. Ward, Andrew P. Jardine, John Ellis, William Allison, Bruno Eckhardt, Gregor Witte

Nature Materials 15 (4), 397-400 (2016) • DOI: 10.1038/nmat4575

https://www.uni-marburg.de/fb13/researchgroups/molecular-solid-state-physics/methods/methods_md?language_sync=1

Hoping this will be helpful,

Rafik

Thank you very much. Rafik

Almost any MD software can give you output coordinates which can be analyzed with another software. Me, I use HOOMD for the molecular dynamics, and then analyze the trajectories with VMD. You can use other MD software too like LAMMPS, NAMD, etc...

If you want to know the distribution in equilibrium and you are not interesting in the dynamics, better to employ some Monte Carlo method. Since I work in adsorption I use RASPA, but any other would work too...

All those softwares let you adjust pressure and temperature.

The easiest way is to use some paid software, like Materials Studio though...

Mr. Bera,

By Gaussian (www.gaussian.com)

Please take a look to the following links:

http://www.gaussian.com/g_tech/g_ur/k_admp.htm

http://www.gaussian.com/g_tech/g_ur/k_bomd.htm

What about Gromacs MD simulation software?

Of course you can do it with GROMACS too (although LAMMPS might be easier...)

Thank you, Fernando