User’s guide

In the user’s manual you will find how to download, build and install the PUPIL software. It also explains how to set up a computation and complete a calculation.
PUPIL v3.1 User’s guide in pdf format (v9.0a October 30,2016).

Standard Citation

Scientific papers and presentations which incorporate results using PUPIL must reference the code as follows:

“PUPIL, Program for User Package Interface and Linking, version 3.1, a software product of the Universitat Politècnica de Catalunya, J. Torras, E. Deumens, S.B.Trickey, H-P.Cheng, C.Cao, Y. He, K. Muralidharan, A. Roitberg, G. Seabra, B. P. Roberts, O. Bertran and Z. Fu.”

and also cite at least one of the four papers about PUPIL listed in the paragraph of the Publications section.


  1. Using PUPIL to postprocess a MD trajectory obtained by Amber with a QM method from Gaussian03 Gustavo Seabra and Ben Roberts (2009). Updated December 2014.


A more complete understanding of the PUPIL architecture and its capabilities can be found in the following PUPIL publications:

  1. Software integration in multi-scale simulations: the PUPIL system , J. Torras, E.Deumens, S. B. Trickey, “ Perspectives on simulations of Chemo-mechanical Phenomena ”, J. Computer Aided-Materials Design, 13, (2006) 201-212.
  2. PUPIL: A systematic approach to software integration in multi-scale simulations, J. Torras, Y. He, C. Cao, K. Muralidharan, E. Deumens, H.-P. Cheng, S. B. Trickey, Computer Physics Communications, 177, (2007) 265-279.
  3. A versatile AMBER-Gaussian QM/MM interface through PUPIL. J. Torras, G. M. Seabra, E. Deumens, S.B. Trickey and A.E. Roitberg. Journal Computational Chemistry, 29, (2008) 1564-1573.
  4. PUPIL: A Software Integration System for Multi-Scale QM/MM-MD Simulations and Its Application to Biomolecular Systems. J. Torras, B.P. Roberts, G.M. Seabra and S.B. Trickey, Adv. Protein Chem. Struct. Biol. 100, (2015) 1-31.


- Original Design
Torras, Juan - EEBE, Univ. Politècnica de Catalunya, Spain
Deumens, Erik - QTP, University of Florida, USA
Trickey, Samuel B. - QTP, University of Florida, USA
- List of contributors (alphabetical order):
Bertran, Oscar - EEI, Univ. Politècnica de Catalunya, Spain
Cao, Chao - HNU, Hangzhou Normal University, China
Cheng, Hai-Ping - QTP, University of Florida, USA
Deumens, Erik - QTP, University of Florida, USA
Fu, Zheng - LJIAI La Jolla Institute for Allergy and Immunology
He, Yao - YNU, Yunnan University, China
Muralidharan, Krishna - Matl. Sci. Eng., University of Arizona, USA
Roberts, Benjamin - UOA, University of Auckland, New Zealand
Roitberg, Adrian - QTP, University of Florida, USA
Seabra, Gustavo M. - DQF, Universidade Federal de Pernambuco, Brazil
Torras, Juan - EEBE, Univ. Politècnica de Catalunya, Spain
Trickey, Samuel B. - QTP, University of Florida, USA
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