Dear All,
I am good at MD simulations with AMBER, NAMD, Gromacs, Forcite... But not familiar with MC simulation. Could you suggest some MC simulation packages? I have to calculate the binding energy of copper MOFs and small molecules at different temperatures.
Thanks,
Xiaoquan.
Check out Cassandra and Towhee. They are two well known ones. There are others though. Cassandra is perhaps the most modern. I have never personally used them for MOF's, but I think Cassandra can do them. I am not sure about Towhee.
https://cassandra.nd.edu/
http://towhee.sourceforge.net/
Both are in written Fortran if you care about looking under the hood. Towhee is Fortran 77 with elements of Fortran 90, and I would say Cassandra is Fortran 90 and newer.
There is also this set of Java Applets by David Kofke that he uses for teaching purposes if you prefer programs written in that language. I am not sure if it is set up to do what you want.
http://www.eng.buffalo.edu/~kofke/ce530/Applets/applets.html
Cheers,
Braden
See the attached paper benchmarking popular MC codes for adsorption on MOFs. Music & RASPA particularly designed for MOFs simulation. If you want to use staged free energy calculation ( i.e, FEP, TI, BAR) for binding energy calculation, note that such methods are not implemented into MC packages (Towhee does TI calculations, but inefficient). Also check out the adaptive biased force calculations in NAMD for binding free energy calculation.
Thank you very much for the reply. It seems the results from different MC packages do not have the siginificant difference for the same system. I am going to learn Cassandra first because the website looks good : )
Hello Chris,
How are you? It is good to find your post here. I wonder how you study Cassandra. I want to study but it is confused me a lot. I read manual and tutorials but many thing unclear. I don't even know how to install it into Ubuntu so I am looking for help. I wonder if some one can give me some help. Thank you
It might be a late reply... but you might want to give a look at DL_MONTE 2.
Check on the webs:
https://www.ccp5.ac.uk/DL_MONTE
and
https://dl_monte.gitlab.io/dl_monte-tutorials-pages/tutorial0.html
And there is also GOMC, which has many features, including the ability to do free energy calculations, and it's fast: http://gomc.eng.wayne.edu/
You may find MC simulator inside LAMMPS package.
There is another simulator developed by the same group, but specifically for MC and Kinetic MC simulations (SPPARKS).
Try BOSS. However, for Monte Carlo's simulation,most of us write their own codes.
You can also try GPU-Optimized Monte Carlo (GOMC). You can simulation adsorption and absolute free energy calculation using FEP and TI.
https://gomc.eng.wayne.edu/
https://github.com/GOMC-WSU/GOMC
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