Our Services

We provide an online platform to perform Coarse-grained molecular dynamics simulations. Users can generate and retrieve necessary input files to run simulations locally. Moreover, the server offers user freedom to modify the parameters according to the need of the experiment.

Perform CGMD

User can run CGMD using our interactive web user interface.

Input preparation

We allow user to creat input files which can be downloaded on the local system.

Download result archieve

After completion of the CGMD simulation, user can download the result directory on local sytem.

Basic analysis

Through MERMAID webserver, we provide basic analysis on the CGMD output of the user.

Frequently Asked Questions

Because it is good that you have planned to study Coarse-grained molecular dynamics simulations. It provides a simplified graphical user interface for the preparation of the required input files to perform Coarse-grained molecular dynamics simulations.
MERMAID is a web service which helps the users to prepare and run Coarse-grained simulations for their studies in computational studies.
MERMAID accepts two kind of files. The first required file is the PDB file for the protein membrane that can be either obtained from the RCSB database or the OPM server (database of membrane proteins). If the user provides the PDB file from the RCSB database, it will be necessary to align the membrane protein structure to its Z-axis before submitting the PDB file to MERMAID. The second file required for running MERMAID is DSSP file. The user can obtain DSSP file of their membrane protein from the online server XSSP.

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