Dec 15 2022

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.