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Simulation in a vacuum for tweaking parameters
- roshan2004
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2 years 2 months ago #9302
by roshan2004
Simulation in a vacuum for tweaking parameters was created by roshan2004
Hi all, I am trying to parametrise a macromolecule using martini. For the sake of saving some computational time, I am thinking of simulating it in vacuum. So, I am just wondering what are the changes we need to make in our current martini3 mdp files(minimization, equilibration, and production) to do so. I am sure we need to off pressure coupling, and all pressure related components. What else changes we need to make? Also, I guess, we need to make a giant periodic box, hoping that it doesn't interact with its periodic copies, but how big should a box be? Any initial guess I can make for making a large box? Thanks.
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- riccardo
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2 years 2 months ago #9309
by riccardo
Replied by riccardo on topic Simulation in a vacuum for tweaking parameters
If you're talking about a polymer, look at the polymer contour length (distance of polymer from end to end when fully stretched) and be sure to have a box so that the polymer can't interact with itself (i.e., the shortest distance in the box should be *at least* larger than the contour length + nonbonded cutoff; I would then try to be on the safe side by adding at least 1-2 nm on top of that estimate).
You don't need any other change besides switching off the pressure coupling. However, are you going to parametrize bonded parameters in this way? Bonds and (maybe) angles won't be affected too much (or at all) by the lack of solvent but dihedrals may very well be. When in a vacuum, your macromolecule will most likely rapidly collapse into a globular aggregate and this will affect the sampling of bonded distributions such as torsional degrees of freedom.
You don't need any other change besides switching off the pressure coupling. However, are you going to parametrize bonded parameters in this way? Bonds and (maybe) angles won't be affected too much (or at all) by the lack of solvent but dihedrals may very well be. When in a vacuum, your macromolecule will most likely rapidly collapse into a globular aggregate and this will affect the sampling of bonded distributions such as torsional degrees of freedom.
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