DLPGEN: The Route to Prepare Molecular Dynamics Simulations
Creators
- 1. Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade de Lisboa
Description
DLPGEN is a Fortran program that produces input files for DL_POLY, GROMACS, LAMMPS, and CHARMM. The program can create simulation boxes with the molecules arranged in a crystalline structure or dispersed in an expanded matrix. To build crystalline materials, data from single-crystal X-rays are required (i.e., unit cell parameters, symmetry operations, and the molecule reduced coordinates). For this purpose, the program reads COORD files, that can be retrieved from the Cambridge Structural Database, or can be manually built using any other data source (e.g., CIF files). As an alternative to these options, PACKMOL can also be automatically called from DLPGEN to create simulation boxes for liquids.
The program can handle force fields like OPLS, CHARMM, and AMBER. Additionally, polarization can also be included in the model. A description of the program functionalities can be found in the following publication:
C.E.S. Bernardes; J. Chem. Inf. Model. 2022, ASAP. https://doi.org/10.1021/acs.jcim.1c01431.
This publication includes the program release 3.1.1 and the corresponding user manual.
Input files to prepare simulations, ca. for ionic liquids, can be found in the following link:
https://webpages.ciencias.ulisboa.pt/~cebernardes/dlpgen_prog/Software_dlpgen_ff_files.html
Video tutorials with step-by-step instructions on how to use the program can be found on Youtube or through the link:
https://webpages.ciencias.ulisboa.pt/~cebernardes/dlpgen_prog/Software_dlpgen_tutorials.html
This work was supported by Fundação para a Ciência e a Tecnologia (FCT), Portugal (projects 021.03239.CEECIND, PTDC/QUI-OUT/28401/2017, LISBOA-01-0145-FEDER-028401, LA/P/0056/2020, UIDB/00100/2020 and UIDP/00100/2020).