normal goMartini for membrane proteins : Time step ?

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3 years 11 months ago #8505 by jpacalon
Hello everyone,

I recently found this quite interesting article ( pubs.acs.org/doi/full/10.1021/acs.jctc.6b00986 ) about using LJ potentials instead of harmonic ones to maintain secondary structure. According to their authors, you can see folding/unfolding of proteins.

So I followed their tutorials (here: info.ifpan.edu.pl/~panos/panos/GoMartini.html ) and effectively, in on of my system quick test I can see the beggining of a-helix folding. Really exited about this.

My (noob) question is regarding the time step to use in martini CG simulations in general. In their tutorials, they put 10fs, but I saw in the Martini tutorials that the time-step can be put as high as 40fs.

What are the factors that limit us to increase the time step? I understand that the highest the time step is, the more chance you have to crash your system and create instabilities. But can I do a trial/error of increasing the time step until my system crash?

Maybe my question would be clearer this way: If I increase the time-step at the maximum value (just before my md crash), does this higher time-step will create errors or artifacts?

Bests !

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3 years 11 months ago #8507 by siewert
Replied by siewert on topic goMartini for membrane proteins : Time step ?
See the FAQ page, there is some description about the choice of time step ....

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