@afranceschem.bsky.social
56 followers 57 following 14 posts
🧪⚡️☀️⏰️ Photochemistry and chemical dynamics. Chemist at University of Valencia #Photochemistry #ExcitedStates #MolecularDynamics
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afranceschem.bsky.social
🔎easyPARM is officially presented in JCTC!! ✅️ Check out the validation and new capabilities 🔆 Great work of A. Abdelgawwad, code developer.
doi.org/10.1021/acs....
#JCTC #CompChem #MetalComplex #MolecularDynamics
easyPARM: Automated, Versatile, and Reliable Force Field Parameters for Metal-Containing Molecules with Unique Labeling of Coordinating Atoms
The dynamics of metal centers are challenging to describe due to the vast variety of ligands, metals, and coordination spheres, hampering the existence of general databases of transferable force field parameters for classical molecular dynamics simulations. Here, we present easyPARM, a Python-based tool that can calculate force field parameters for a wide range of metal complexes from routine frequency calculations with electronic structure methods. The approach is based on a unique labeling strategy, in which each ligand atom that coordinates the metal receives a unique atom type. This design prevents parameter shortage, labeling duplication, and the necessity to post-process output files, even for very complicated coordination spheres, whose parametrization process remain automatic. The program requires the Cartesian Hessian matrix, the geometry xyz file, and the atomic charges to provide reliable force-field parameters extensively benchmarked against density functional theory dynamics in both the gas and condensed phases. The procedure allows the classical description of metal complexes at a low computational cost with an accuracy as good as the quality of the Hessian matrix obtained by quantum chemistry methods. easyPARM v2.00 reads vibrational frequencies and charges in Gaussian (version 09 or 16) or ORCA (version 5 or 6) format and provides refined force-field parameters in Amber format. These can be directly used in Amber and NAMD molecular dynamics engines or converted to other formats. The tool is available free of charge in the GitHub platform (https://github.com/Abdelazim-Abdelgawwad/easyPARM.git).
doi.org
afranceschem.bsky.social
Deeply honored to the ESP for the young investigator award #ESPcongress2025
@photobiologyeurope.bsky.social
afranceschem.bsky.social
Listening to Sherri McFarland's plenary lecture. Top science! #ESPcongress2025
afranceschem.bsky.social
All ready to start the #ESPcongress2025. Hi Bari!!
afranceschem.bsky.social
Deeply honoured to receive this award. Thank you @photobiologyeurope.bsky.social !!! See you in Bari
photobiologyeurope.bsky.social
🥁 Drum roll........the 2025 Young Investigator Awardees have been selected! Congratulations to Nicoletta Liguori @nikinikki87.bsky.social and Antonio Francés-Monerris @afranceschem.bsky.social 🎉 They will deliver the Young Investigator Award Lectureship at the #ESPCongress2025. See you all there!
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letigonzalez.bsky.social
18 positions with one more in theory!
📣📣📣
Fancy theory, catalysis , excellent research, and working in the most liveable city of the world?
🖥️☀️🎓🇦🇹
Apply now!
#phdjobs
univie.ac.at
Vienna Doctoral School in #Chemistry offers 17 fully funded #PhD positions. 🧪 #phdsky #academicsky 👩‍🔬👨‍🔬
📅 Application deadline: April 21, 2025.
For more information & how to apply: ⤵️
doschem.univie.ac.at/application/...
Vienna Doctoral School in Chemistry - DoSChem call 2025. We offer 17 fully funded PhD positions in Chemistry. Application Deadline: 21.04.2025.
Reposted
agandioso.bsky.social
🧪📣❗ #PhDPosition to develop light-activated drugs for cancer phototherapy. We are seeking candidates with a strong background in #OrganicChemistry #ChemBio and #MedChem to apply for FI-STEP predoctoral fellowships #PDT #Metallodrugs #ScienceJobs
Reposted
elisedd.bsky.social
Job alert ! I am looking for a postdoc to work on "computational investigation of ion-effects in ribozyme catalysis" to work with me in Paris (France). 1-year contract funded by @agencerecherche.bsky.social, with possible 2nd year in collab. with P. Jungwirth @iocbprague.bsky.social #compchem #RNA
Reposted
huixrotllant.bsky.social
A PhD position in theoretical chemistry (2025-2028) is available in my group starting in October. Info&Apply: huixrotllant.github.io/openings.html #academicjobs #compchem Please RT
Openings
huixrotllant.github.io
afranceschem.bsky.social
🔎easyPARM is officially presented in JCTC!! ✅️ Check out the validation and new capabilities 🔆 Great work of A. Abdelgawwad, code developer.
doi.org/10.1021/acs....
#JCTC #CompChem #MetalComplex #MolecularDynamics
easyPARM: Automated, Versatile, and Reliable Force Field Parameters for Metal-Containing Molecules with Unique Labeling of Coordinating Atoms
The dynamics of metal centers are challenging to describe due to the vast variety of ligands, metals, and coordination spheres, hampering the existence of general databases of transferable force field parameters for classical molecular dynamics simulations. Here, we present easyPARM, a Python-based tool that can calculate force field parameters for a wide range of metal complexes from routine frequency calculations with electronic structure methods. The approach is based on a unique labeling strategy, in which each ligand atom that coordinates the metal receives a unique atom type. This design prevents parameter shortage, labeling duplication, and the necessity to post-process output files, even for very complicated coordination spheres, whose parametrization process remain automatic. The program requires the Cartesian Hessian matrix, the geometry xyz file, and the atomic charges to provide reliable force-field parameters extensively benchmarked against density functional theory dynamics in both the gas and condensed phases. The procedure allows the classical description of metal complexes at a low computational cost with an accuracy as good as the quality of the Hessian matrix obtained by quantum chemistry methods. easyPARM v2.00 reads vibrational frequencies and charges in Gaussian (version 09 or 16) or ORCA (version 5 or 6) format and provides refined force-field parameters in Amber format. These can be directly used in Amber and NAMD molecular dynamics engines or converted to other formats. The tool is available free of charge in the GitHub platform (https://github.com/Abdelazim-Abdelgawwad/easyPARM.git).
doi.org
afranceschem.bsky.social
So glad it helps! A new version (v3.00) has been recently released with new features
afranceschem.bsky.social
Here we introduce easyPARM, a free code to generate force field parameters for transition metal complexes. The program requires only the Gaussian/ORCA frequencies and the RESP charges. The output is in Amber format.
chemrxiv.org/engage/chemr...