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Molecular mass optimazation
- nanogod
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13 years 4 months ago #448
by nanogod
Molecular mass optimazation was created by nanogod
Hi, I was thinking about optimizing the mass of the different beads in martini_v2.P.itp, but I am wondering about the consequences.
At the moment I am doing md simulations with time steps of 0.025 ps, I guess that I would have to use smaller steps but how much smaller?
Furthermore; This should yield a more accurate md simulation, but is that worth it if I plan to convert my final state to fine grain and run a fine grain md simulation for about 5 ns ?
Thanks for the help
Morten
At the moment I am doing md simulations with time steps of 0.025 ps, I guess that I would have to use smaller steps but how much smaller?
Furthermore; This should yield a more accurate md simulation, but is that worth it if I plan to convert my final state to fine grain and run a fine grain md simulation for about 5 ns ?
Thanks for the help
Morten
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- xavier
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13 years 4 months ago #449
by xavier
Replied by xavier on topic Molecular mass optimazation
Dear Morten,
In principle it is a good idea to refine the masses in Martini. The main side effect in having the standard 72 UMA per bead is that the dynamics of the system might be altered because the mass of your system is not exact (often to high). It is however not clear how strong the effect is. This is not expected to be significant but it has not been systematically investigated (yet).
You might indeed need to reduce the time step to keep your simulation stable. How much is function of the changes you'd have to make.
The worth of the effort would be function of what you are looking at and what you like to measure ...
Not much more we can say at that point :))
XAvier.
In principle it is a good idea to refine the masses in Martini. The main side effect in having the standard 72 UMA per bead is that the dynamics of the system might be altered because the mass of your system is not exact (often to high). It is however not clear how strong the effect is. This is not expected to be significant but it has not been systematically investigated (yet).
You might indeed need to reduce the time step to keep your simulation stable. How much is function of the changes you'd have to make.
The worth of the effort would be function of what you are looking at and what you like to measure ...
Not much more we can say at that point :))
XAvier.
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