T83-2022 Notification regarding BIOVIA Materials Studio 2023
BIOVIA Materials Studio
Technical Note T83-2022
December 2022
Notification regarding BIOVIA Materials Studio 2023
Program
BIOVIA Materials Studio
Operating System
All supported operating systems
Description
We are providing this Technical Note to inform you about the release of BIOVIA Materials Studio 2023 which includes the following enhancements and fixed defects:
Enhancements
This release of BIOVIA Materials Studio includes the following enhancements.
User Story | Description |
MS-32974 | Mesocite DPD now supports electrostatics by allowing the smearing of bead charges using a Gaussian distribution. |
MS-32975 | Mesocite and Forcite analysis now support calculation of the structure factor from a density field. |
MS-39359 | CASTEP linear response calculations of vibrational properties are implemented for spin-polarized (magnetic) systems. |
MS-51020 | Mesocite and Forcite analysis now support pressure analysis with anisotropic components. |
MS-55751 | Scripting now recognizes SMILES and chemical names for molecules and fragments. A script to analyze the content of a simulation cell or the development of different reagents over the course of a trajectory is also available. |
MS-57707 | The controls for working with protocols are now at the top of the Pipeline Pilot Protocols dialog so that you can manage the size and location of the dialog more easily. |
MS-57720 | CASTEP DFT+U no longer requires a spin-polarized setting for systems that are not magnetic, making such calculations at least a factor of two faster. |
MS-58409 | The COSMO implicit solvation model is now available in DFTB+. |
MS-58725 | Martini 3 Tools have been enhanced and include a new MS Martini 3 Coarse Grainer function that generates a Mesostructure model from an atomic model including bead mapping and forcefield typing using a template study table. This functionality allows you to generate Mesostructure models along with a customized MS Martini 3 forcefield including the valence terms. |
MS-58838 | The meaning of the integrated crystal orbital Hamiltonian populations, COHP, is explained in the DMol3 documentation. |
MS-58849 | The GULP "Calculating the properties of diamond" tutorial now reflects the current state of the application. |
MS-58861 | The Pipeline Pilot Protocols dialog now reports the version of Materials Studio Collection installed on the Pipeline Pilot server. |
MS-58916 | The DFTB+ server is updated to version 22.1. As a consequence of this upgrade Debug (client side) scripting using DFTB+ is no longer possible. |
MS-58928 | Forcite GPU calculations now support the Embedded Atom Model. |
MS-58929 | A review of the Forcite dynamics GPU algorithms has resulted in updates providing significant performance enhancements. |
MS-59027 | You can now access a range of prepared MaterialsScript tools from Tools > Materials Studio Scripts in the menu bar. These scripts were previously provided as examples to manually add to the User menu. |
MS-59037 | You can now fit polynomial potential terms for two-body interactions in GULP up to the eighth order. |
MS-59188 | You can now access a set of Quantum Chemistry protocols that provide TURBOMOLE workflows through the Pipeline Pilot Protocols dialog. |
MS-59268 | Force calculations in the presence of implicit solvent are now available in CASTEP. This allows you to perform geometry optimization, molecular dynamics, and other tasks taking into account the effect of solvents. |
MS-59274 | A periodic version of the novel universal forcefield GFN-FF is now implemented in GULP. This is a fully automated polarizable forcefield with nearly quantum-mechanical accuracy, as described in J. Gale et al., J. Chem. Theory Comput. 17 (2021) 7827–7849 |
MS-59382 | You can now configure a local gateway running on your Materials Studio client computer not to use Apache while retaining full gateway functionality for local users. |
MS-59585 | The icon for the CCDC module in the Materials Studio toolbar now has a more modern look and feel. |
MS-59609 | You can now access a set of prepared MS Martini 3 scripts from _Tools > Materials Studio Scripts_ in the menu bar. |
MS-59613 | Materials Studio documentation has now a new tutorial demonstrating the usage of Polymer Coarse Graining with Martini 3 Tools to build mesostructure starting from an all-atom model and generate custom MS Martini 3 forcefield using bead mapping templates. The tutorial also explains how to create custom bead mapping templates and use the Mesocite module to run dynamics simulation with the mesostructure and the custom MS Martini 3 forcefield generated using the protocol. |
MS-59807 | The new CERIA and TiO2nano parameter sets provide support for some additional metal oxides in DFTB+. |
MS-59824 | The hybrid exchange-correlation functional implementation in ONETEP now extends to cover 3D periodic systems, not just "molecule in a box" geometries. |
MS-59833 | The ONETEP server is upgraded to version 6.1.12. |
MS-59834 | The GULP server is updated to version 6.1. |
MS-60264 | There is a new tutorial demonstrating the usage of Coarse Grain and Generate Custom Martini3 Forcefield protocol to build mesostructure starting from an all-atom model and generate custom MS Martini 3 forcefield using bead mapping templates. The tutorial also explains how to create custom bead mapping templates and use the Mesocite module to run dynamics simulation with the mesostructure and the custom MS Martini 3 forcefield generated using the protocol. |
MS-58881 | FlexTS path trajectories are now provided in the correct order. The NEB path thresholds in FlexTS now ensure more stable convergence for complex reaction pathways. The workflow in the "Calculating the Minimum Energy Path of a molecular switch" tutorial for DMol3 and DFTB+ has been improved. |
MS-58884 | The COMPASSIII water model now provides an improved prediction of diffusion coefficients. |
MS-58926 | You can now run Mesocite Dissipative Particle Dynamics (DPD) calculations on NVIDIA GPUs. |
Fixed Defects
This release of BIOVIA Materials Studio includes the following fixed defects.
User Story | Description |
MS-58921 | Materials Studio no longer freezes when trying to connect to an unresponsive Pipeline Pilot Server. |
MS-58988 | Forcite Radial Distribution Function analysis now supports systems with more than 65 000 atoms. |
MS-59170 | Stress evaluation in CASTEP using nonlocal hybrid functionals is improved. You can now calculate stresses and perform tasks that require the stress tensor (cell optimization, variable cell molecular dynamics, elastic constants calculation) using any nonlocal or hybrid exchange-correlation functional. CASTEP no longer uses a constant shift in energy (the Hartree-Fock divergence correction) when applying nonlocal exchange-correlation functionals to insulators or semiconductors. This divergence correction only impacts Hartree-Fock calculations where a band crosses the Fermi level and creates a singularity in the potential. As a result of this change, the total energies calculated with fixed electronic occupancies differ from previous versions of Materials Studio. The new results are more physical and produce total energy that is consistent with the stress tensor. |
MS-59418 | Support for the PBS Pro queuing system on Windows is discontinued. |
MS-59455 | CASTEP DFT+U calculations of the stress tensor for cubic systems no longer return inconsistent values. |
MS-59516 | The CreateSet function no longer allows you to create multiple sets with the same name. |
MS-59550 | Polymorph Prediction calculations no longer terminate with an unhelpful error message if they find no structures for a particular space group. |
MS-59656 | You can now adjust the phonon q-point mesh for linear interpolation so that it is commensurate with the electronic k-point grid in CASTEP phonon calculations. |
MS-59673 | Using GPU in Forcite to calculate the Morse dispersion interaction no longer gives an incorrect result. |
MS-60006 | Trajectories generated by FlexTS now automatically monitor bonding to display reactions. |
MS-60072 | The version of Apache deployed in the Materials Studio Gateway has been updated to 2.4.54 for both Windows and Linux operating systems. |
MS-57193 | Forcite now allows 1-4 van der Waals scaling for the 1-4 pairs of missing torsion terms. If you specify Ignore for a torsion term, then Forcite always fully scales the 1-4 van der Waals interactions, independent of the choice of the exclusion of van der Waals 1-4 scaling. |
MS-57891 | When the sequence of forcefield types is symmetric, certain forcefield functional forms logically require certain parameters to be equal. For example, the two constants of the stretch-bend-stretch interaction must be the same when the i and k atoms have the same type. The forcefield MaterialsScript API now enforces these constraints by reporting an error for illegal parameter value combinations. |
MS-58110 | Long DFTB+ molecular dynamics simulations running in parallel no longer fail after a large number of steps. |
MS-58204 | Amorphous Cell Packing now correctly checks for ring spearing in structures with a shifted origin. |
MS-58609 | When exporting documents to previous versions, the list of supported previous versions has been set to Materials Studio 2020 and later versions. |
MS-58814 | The forcefield browser in the Mesocite dialog no longer reports an error when trying to select a forcefield with a long name. |
MS-58860 | Reflex Powder Refinement dialog no longer reports an error in the scenario when the atoms tab was populated from a structure document and then the dialog is closed after the structure document is closed. |
MS-58890 | The Cohesive Energy Density task in Forcite now correctly handles negative CED contributions. |
MS-59008 | The CASTEP NMR results file is now correctly formatted for large systems (more than 100 atoms). |
MS-59031 | The charges in COMPASSIII for the hydroxide anion have been corrected. |
MS-59167 | The mechanism for generating names of temporary folders is improved to avoid runtime clashes when running CASTEP and QMERA jobs. |
MS-59190 | Materials Studio now correctly sets the MBD* method for DFT CASTEP calculations. |
MS-59297 | The long-range correction for the Morse potential with default parameters now returns 0. |
MS-59300 | The Materials Studio error when importing an xyz file with a very long comment line has been corrected. |
MS-59316 | Materials Studio now uses more robust file system libraries for job management. |
MS-59337 | Materials Studio is now blocking attempts to start DFT+U CASTEP calculation with non-collinear spin arrangements |
MS-59352 | It is now possible to use ReactionFinder on the secure gateways |
MS-59459 | A bug has been fixed such that you can now analyze the structure evolution for a geometry optimization after doing a Raman analysis in the same run. |
MS-59580 | You can now run scripts using Forcite and Mesocite on a GPU from the command line (that is, using RunMatScript.sh) by specifying the UseGPU scripting property. |
MS-59621 | The help topic on the MaterialsScript API Scattering function for Forcite analysis no longer indicates that the ScatteringWavelength property only applies to neutron radiation. |
MS-59684 | Large bead masses can now be entered on the Bead Types dialog. |
MS-59751 | The example TBL file in the visualizer documentation is amended to conform to the format that is supported in Materials Studio. |
MS-59954 | The Generating an MS Martini 3 Forcefield and Bead Topology tutorial procedure now uses the tools in the newly introduced Materials Studio Scripts menu. |
MS-60117 | The reference images of the Remote Gateway Web Page in the Materials Studio Online Help are now updated. |
MS-60151 | The Generating a MS Martini 3 Forcefield and Bead Topology tutorial reflects the recent enhancements to Martini 3 Tools and shows you how to use the prepared scripts provided in the Materials Studio Scripts menu. |
MS-60207 | CASTEP TD-DFT calculations with non-Gamma k-point sampling of the Brillouin zone now complete successfully. |
MS-60239 | GULP forcefield fitting using multiple unrelaxed configurations and phonon frequencies as observables now completes successfully. |
MS-57167 | COMPASSIII now predicts planar geometry for furoxan in all resonance forms. |
MS-57294 | Some default bond stretch interactions for the o1-_ type have been added to COMPASSIII. |
MS-58076 | The Forcite potential energy components analysis can now be used on trajectory documents (xtd) based on the xyz file format. |
MS-58098 | The Job Complete dialog for Pipeline Pilot Protocol jobs now displays on top of the Materials Studio Visualizer window. |
MS-58189 | The QSAR Model Editor dialog now correctly checks the input against the allowed range. |
MS-58996 | The Adsorption Locator documentation now clearly describes the system's state used in the calculation of the energy of substrate-adsorbate configurations. |
MS-59017 | Occasional errors encountered for the Forcite and Mesocite Analysis dialogs when running some particular scripts in debug mode have been addressed. |
MS-59036 | The COMPASSIII interactions in sulfur hexafluoride and thioformaldehyde have been corrected. |
MS-59052 | The torsion interaction in COMPASSIII for perfluoroalkanes has been updated. |
MS-59059 | The scripting API F1 help lookup now contains a direct link to the documentation of the StudyTable class. |
MS-59132 | The Create DPD Forcefield dialog now generates forcefield type names with 6 characters, instead of 5. |
MS-59140 | Calculation of the electrostatic and van der Waals forces between charge groups at close proximity no longer suffers from discontinuity. |
MS-59208 | Forcite no longer calculates incorrect energy and forces for certain continuous periodic structures with scaled 1-4 nonbond interactions. |
MS-59237 | The Materials Studio installer now installs some additional libraries before starting, this prevents errors from occurring during the installation process. |
MS-59252 | The help topic on the Types tab of the Forcefield Viewer now includes a link to the task describing how to create and edit types. |
MS-59381 | CASTEP output of Berry phase polarization now uses the correct label for the output range of computed values. |
MS-59384 | For the French locale, the interaction values on the MesoDyn Calculation dialog are now correctly formatted. |
MS-59404 | The Radial Distribution Function analyses in Forcite and Mesocite now include the module name in the chart and study table documents generated for the structure factor. |
MS-59504 | The Build Mesostructure dialog now correctly handles the filler names that use mismatched cases compared to those available. |
MS-59695 | The long name of space group 221 was previously shown incorrectly as "P M -3 M". The correct name "P 4/M -3 2/M" is now shown. Note that the CrystalBuilder scripting API also accepted the incorrect form, so scripts may need to be changed to use either the short form or the correct long form. |
MS-59876 | The MaterialsScript documentation now includes information on using reciprocal vectors. |
MS-59925 | On the Forcefield Preferences dialog, when you specify the van der Waals and electrostatic 1-4 scaling factors with 5 significant figures, these now display correctly. |
MS-59973 | An example structure is now provided in the first step of the "Calculating the Minimum Energy Path of a molecular switch" DFTB+ and DMol3 tutorial. |
MS-59979 | The instructions for the tutorial "Calculating the Minimum Energy Path of a molecular switch" have been improved. |
MS-59991 | The refresh of the Grid resolution dropdown list in the DFTB+ Grid Parameters dialog is now correct. |
MS-60011 | The Reaction Pathway Display protocol help now includes an explanation of how to specify the energy offsets to customize the output. |
MS-60023 | The Materials Studio online help now includes information on how to use the entire contents of the 3D Model Document as a MaterialsScript collection. |
Resolution
BIOVIA Materials Studio 2023 was released in December 2022 and is available for download at https://software.3ds.com under BIOVIA products and can be found under:
Product line: Lab, Scientific and Content Solutions
Release: BIOVIA 2023
Level: BIOVIA 2023 Golden
How to contact BIOVIA Support
If you have any questions, please contact BIOVIA Support.