Hi,
I would like to run MD simulation of a membrane protein using GROMACS or NAMD. However, my institute does-not have high configuration systems, and I have no financial support for purchasing them. I have seen a few websites like MDWEB, CHARMM-GUI and software like jSimMacs with which I can run MD simulations remotely. I would like to know which web server functions optimally and in which servers I can manually edit some features like number of steps for energy minimization, etc.
Please let me know if there are any other web servers to run MD simulations.
Thanks.
I would like to study the drug reflux activity of the protein. I also want to find any intermediate states of drug-protein complex.
Yes, you can use web-server MD, provided it has published article that described its development and operation, of which you can cite as reference for your work.
However, GROMAC is free and run easily on linux OS computer (laptop or desktop).
I recently found these servers.
http://haddock.science.uu.nl/enmr/services/GROMACS/main.php
http://mmb.irbbarcelona.org/MDWeb/
http://biocomp.chem.uw.edu.pl/CABSflex/
http://vienna-ptm.univie.ac.at
https://mosgrid.de/help/molecular-dynamics
Directory of simulation server can be found here:
http://www.vls3d.com/index.php/links/bioinformatics/simulation
Kind regards.
Toluwase H. Fatoki
Hi
Have a look at following MODSIM.
Helpfully it will be help you
http://open.gpcr-modsim.org/
I agree with Toluwase H. Fatoki ; i already used 2 of the sites sited above;
Regards;
Joseph
Hello,
My group developed a web interface for LAMMPS, all jobs are run in the Purdue University computer cluster. You need to provide your own LAMMPS script and potential files.
Please take a look at https://nanohub.org/tools/lammpstool
Regards,
David
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