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: —

Viewer loading...

Conformer
0/0
Isomer
0/0

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.

Running…
Format

##### Pair Distance Histogram

##### Pair Distance Statistics

Track Running Job

A job is running. Track its live output below.

Select a mode to animate

Mode

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.

### Energy vs Time Step

0 selected
Jobs: 0 Storage: 0 MB

Track all jobs submitted to this server. Queue order is FIFO across users.

| 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

## README documentation

The project documentation will appear here after it loads.

### Periodic Table

### GNU General Public License v3.0

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