normal ion channel

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7 years 7 months ago #5787 by ion channel
ion channel was created by ion channel
Hi
I've simulated KcsA ion channel by gromacs 5.1.1. I'm going to investigate dynamics of ions through the selectivity filter of ion channel by molecular dynamics method.
when I repeat a simulation in a similar situation (because of obtaining more data), result of simulation changes.
I don't know what's the matter?

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7 years 7 months ago - 7 years 7 months ago #5807 by bart
Replied by bart on topic ion channel
Hi Ion channel,

In MD the simulations are most of the time not binary reproductive. This means that the same intitial configuration will yield different trajectories upon repeats. However, if your simulation samples enough of the solution space the distribution of states should be preserved. Thus if your results are severely different in their state distribution, you probably did not sample enough. Therefore increasing the simulation length might help.

Cheers,

Bart
Last edit: 7 years 7 months ago by bart.

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7 years 7 months ago #5809 by peterkroon
Replied by peterkroon on topic ion channel
Or, in addition to making the simulations longer: run more independent simulations.

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7 years 7 months ago #5838 by xavier
Replied by xavier on topic ion channel
What do you observe changing?

Simulating the transfer of ions through channels might be tricky with Martini. You may want to describe your approach to get better feedback.

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7 years 5 months ago #5995 by ion channel
Replied by ion channel on topic ion channel
Hi
Thanks for your answer.
I increased simulation samples but the result of first simulation was diffrent from second simulation.
Just in intial for one Ps the trajectory of ions has been same.

best regard

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7 years 5 months ago #5999 by peterkroon
Replied by peterkroon on topic ion channel
Hi,

MD is stochastic, so it is expected to see non identical results for different simulations - this is why it is crucially important to make sure your simulations are converged, and to make sure you don't draw conclusions based on a single simulation.

This also sums up my advise to you: 1) make sure your simulations are converged and 2) run more independent simulations.

Alternatively, you can consider measuring the PMF of an ion being pulled through the pore.

Peter

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