Program for User Package Interface and Linking

Documentation

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 v4.0 User’s guide in pdf format (v10.0d July 31, 2022).

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 4.0, (2022) 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.

Tutorials

1. Using PUPIL to postprocess a MD trajectory obtained by Amber with a QM method from Gaussian03 Gustavo Seabra and Ben Roberts (2009). Updated to PUPIL v4.0.

Publications

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.
   

Contributions