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Simlab

WebGRO

PROTEIN IN WATER SIMULATION

Key Points

Submit only protein molecule for simulation using this tool. If there are missing residues and/or atoms in your proteins, GROMACS preprocessing could throw an error. Please fix those errors before you submit.
This tool follows the general protocol for setting up a simulation of system containing protein in water.
1) Preprocessing.
2) Energy minimiztion.
3) Equilibration.
4) Molecular Dynamics.
5) Trajectory analysis & Results generation.
*For detailed instructions on how to set up submission using WebGro, please click here


File Upload Please upload your PDB file:   
1) Currently we can only simulate systems with less than or equal to 150,000 atoms (including water and other solvent molecules or ions)
2) Any external water (unbound water molecules included with experimental structures) and/or ligands associated with the target protein will be automatically removed before simulation.


Input Parameters EMAIL:

User key:

Register for user key here

Forcefield:

Water model:

Box Type:

Salt Type:

Neutralize add 0.15M salt


Energy Minimization parameters Integrator:

Steps:


Equilibration and MD run Parameters Equilibration Type:   NVT/NPT

Temperature (K):   Range 150 - 400 K
Pressure (bar):    

MD integrator:

Simulation time (ns): (max allowed 50nsec)

Approximate number of frame per simulation:



Simulation Result Analysis RMSD     Computes Root Mean Square Deviation of the given structure over time

RMSF     Computes Root Mean Square Fluctuation of each residue in the given structure

Rg     Computes Radius of Gyration or structural compactness

SASA     Computes Solvent-Accessible Surface Area

Hbonds     Computes average number of H-bonds in each frame over time



WARNING: Do not click the Submit button more than once (or press enter more than once).
Duplicate jobs will be cancelled. To avoid having all your submitted jobs cancelled do not produce duplicates.

Note:
Your email client may place emails from WebGro into the spam folder.
Please check the spam folder and white list all emails coming from UAMS mail servers.
For example, noreply@netmail1.uams.edu and noreply@netmail2.uams.edu