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goMartini for membrane proteins : Time step ?
- jpacalon
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4 years 1 day ago #8505
by jpacalon
goMartini for membrane proteins : Time step ? was created 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 !
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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- siewert
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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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