uma-ase WebApp

Load Atomic System

Load from file

Fetch from ioChem-BD

Create from SMILES

Fetch from PDBe

Fetch from PubChem

Atomic System Details

No structure loaded.

Charge

Multiplicity

Atoms

—

Formula

—

2D structure will appear here.

IUPAC name: —

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Structure: None • Selected atoms: None

Edit

Selected Atom None Chemical Element — will be replaced by

Generate conformers

Single Job Multi Jobs Molecular Dynamics

Input Details

System

Selected input file No file selected

Charge

Spin Multiplicity

Method

UMA Checkpoint

UMA Task

Run Parameters

Run Type

Single Point GeoOpt Frequencies Transition State

Optimizer

Force (eV/Å)

Max GeoOpt Iter

Vibrational Analysis Settings

Temperature (K)

Pressure (atm)

TS Search Settings

Mode displacement (Å)

Dimer separation (Å)

Trial translation (Å)

Max translation (Å)

Max rotations

Results

Select an input file and run a job to see results here.

Input Details

System

Input folder

No folder selected

Select a folder of .xyz files to run them sequentially.

Charge

Used when charge is not encoded in the XYZ comment.

Spin Multiplicity

Fallback spin value for files without metadata.

Method

UMA Checkpoint

UMA Task

Run Parameters

Run Type

Single Point GeoOpt Frequencies Transition State

Optimizer

Force (eV/Å)

Max GeoOpt Iter

Vibrational Analysis Settings

Temperature (K)

Pressure (atm)

TS Search Settings

Mode displacement (Å)

Dimer separation (Å)

Trial translation (Å)

Max translation (Å)

Max rotations

Results

Input Details

System

Selected input file No file selected

Charge

Spin Multiplicity

Method

UMA Checkpoint

UMA Task

Dynamics Parameters

Dynamics Engine

Steps

Timestep (fs)

Trajectory Interval (steps)

Log Interval (steps)

Target Temperature (K)

Friction (1/fs)

Thermostat Relaxation (fs)

Target Pressure (bar)

Compressibility (1/bar)

Barostat Relaxation (fs)

Periodic Boundary Conditions

Apply periodic boundary conditions

Cell a (Å)

Cell b (Å)

Cell c (Å)

Alpha (°)

Beta (°)

Gamma (°)

Nose-Hoover Parameters

Thermostat Damping (fs)

Chain Length

Thermostat Sub-steps

Bussi Time Constant (fs)

Andersen Collision Probability

MTK Parameters

Thermostat Damping (fs)

Barostat Damping (fs)

Thermostat Chain Length

Barostat Chain Length

Thermostat Sub-steps

Barostat Sub-steps

BAOAB Thermostat Tau (fs)

BAOAB Barostat Options

Barostat Tau (fs)

Cell Mass (ASE units)

Mass Factor

Hydrostatic cell (preserve shape)

Melchionna Controls

Thermostat Time (fs)

Barostat Time (fs)

Bulk Modulus (GPa)

Mask (comma separated, e.g. 1,1,1)

MD Output

Upload a structure and configure molecular dynamics options to begin.

Analyze

RMSD Report Reads uma-ase .log files (Formula, RMSD, model, optimizer) and generates a bar plot with a formula table.

Select a folder

Pick a folder containing uma-ase log files.

No folder selected.

XYZ Pair Analysis Matches *.xyz files with their *geoopt-OPT* counterparts in a folder and runs a detailed geometry analysis.

Select a folder

Pick a folder containing XYZ files and geoopt outputs.

No folder selected.

Simple Geometry Analysis Calculates atom-pair distance distributions for uploaded structures.

Select file

Pick a geometry file (.xyz, .mol, .pdb, .cif, ...).

No file selected.

Include distance matrix in report

RMSD Report

Reads uma-ase .log files and builds RMSD summaries by formula.

Format

Open a Downloaded Job

Load UMA .use file

Load uma-ase log (.log)

Open a Trajectory file

Load trajectory / XYZ

No trajectory loaded.

Vibrational Modes

Modes archive (.zip)

No archive selected.

Reference log (.log)

No log selected.

Select the matching -FREQS-modes.zip bundle and its log file to enable normal-mode playback.

30 fps

3D viewer idle. Load a trajectory to begin.

Frame: No frames loaded.

	Status	Name	Job ID	Type	Submitted	Started	Finished	Elapsed	Retention	Actions
No jobs submitted yet.

Login in your ioChem-BD

This operation will generate a key for ioChem-BD/Create operations (expires after 24 hours).

Your ioChem-BD is at:

Paste a host (iochem-bd.iciq.es) or a full /create/rest URL.

Username

normally an email address

Password

Forgot your passwd

Key/JWT token

Keep the key and paste it here to continue operations in case of interruption

Browse ioChem-BD Files

Load your authenticated ioChem-BD file tree (or shared trees), click a folder to set the upload destination, and click a calculation to import its CML.

Root path

Uses the Create REST token above.

No shared projects loaded.

Source: My files

No tree loaded yet.

Upload Results

Upload all your results in a zipped file.

Destination path

Calculation type is fixed to UMA.

Calculation name

Description/Keywords

Session

Login required.

Request Override

Retention days

Max jobs

Max storage

Justification

Request at least one override. Use positive integers for days/jobs and values like 500MB, 1GB, or 2GiB for storage. Justification must contain at least 10 characters.

No override requests submitted yet.

README documentation

The project documentation will appear here after it loads.

uma-ase v0.9.8

Edit

Input Details

Results

Input Details

Results

Input Details

MD Output

Analyze

RMSD Report

Pair Distance Histogram

Pair Distance Statistics

Energy vs Time Step

Login in your ioChem-BD

Browse ioChem-BD Files

Upload Results

About uma-ase

README documentation