normal About the structure froozening in Martini

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9 years 4 months ago #4171 by xiaoyan_zheng
About the structure froozening in Martini was created by xiaoyan_zheng
Hi,

After reading some papers about Maritni force field, I know that the system setup based on Martini force field are easy to frozen at temperature range between 280 K to 300 K. Due to my interested system are based on the experiment performed in room temperature.

I set the temperature in 300 K. When I look at my trajectory, I see all the atoms in the system are in motion state. But I am still not sure whether my system is frozen or not ? That's to say, how to justify whether my system is frozen or not ? Is there much difference for the martini force field perform in 300 K and 320 K?

I need to simulate the self-assembly process of amphiphilic organic molecules, I found that in high concentration, the self-assembly become very solw. Are there any relationship between the frozen to the concentration of the studied system ?

If my system is frozen, could I increase the temperture to 320K, if I increase the temperature to 320 K, how could I compare with the experimental results?

Best Regards,

Xiaoyan

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9 years 2 weeks ago #4484 by Clement
Replied by Clement on topic About the structure froozening in Martini
The frozening effect happens for water (namely, "W") beads, and for relatively small system. It's actually quite rare. If you're afraid of that to happen, you can replace 10% of your water beads by "BW" ("big water) beads. It's enough to break this effect. But if you're not sure to see frozening, then it's not frozen. You'll see it quite clearly when encountered.

I think the slowing down you see is due to the high concentration of your molecule of interest... You can compute a diffusion coefficient with g_msd and check that.

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9 years 2 weeks ago #4488 by xiaoyan_zheng
Replied by xiaoyan_zheng on topic About the structure froozening in Martini
Thanks for your kind explanation and good suggestions. I will be much helpful for me. I will try to do that to check my system carefully.

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