normal Starting MARTINI MD Simulations of Polymers

  • TravisM
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9 months 1 day ago #8339 by TravisM
Hello all,

I am brand new to molecular dynamics simulations, and am interested in trying to learn GROMACS/MARTINI as a means of understanding the structural properties of single-chain polymer nanoparticles. I don't have any prior experience with any kind of computer simulations or even LINUX, so needless to say moving forward seems to be a pretty daunting process.

As of now I do not have access to a mutli-core cluster for running simulations. Is it all feasible for me to work on learning MARTINI simulations using just my laptop? I tried following some generic AA simulation tutorials, but the energy minimization step alone was going to take 13 hours. I can get access in several months to a cluster, but it would be great if I could get started learning now.

Along those same lines, any tips/tutorials/recommendations for a new user?


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8 months 3 weeks ago #8342 by Pim
Hi Travis,

Some people even made some Martini simulations work on their smartphone, so you should be good for the basics, it is really 2-3 orders of magnitude faster than the atomistic equivalent simulations.

If you start with the basic tutorials for Gromacs 5 and newer: lipids, proteins, parametrizing a new molecule you should be good with an average laptop. The polymer melt tutorial may be slightly heavier, but not much. If you encounter any steps that are unacceptably long, try to run them for shorter times, often that is fine too.

Good luck!

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