normal Position restrained water wall

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5 years 11 months ago #1708 by nanogod
Position restrained water wall was created by nanogod
Hey,

I am trying to contain some proteins from interacting with each other throug the x/y direction of the PBC box. I have been trying to do this by having a thin layer of position restrained polarized water along the surface of the x/y box wall.

This works great, but all the proteins are adsorbed to the position restrained water surface! Does any one have an idea of how to avoid this?

I have tried to decouple pressure and temperature of the position restrained water from the rest of the molecules, but the proteins are still adsorbed at the interface.


I really need your help, anyone has any ideas?


Kind regards
Nanogod

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5 years 11 months ago #1712 by djurre
Replied by djurre on topic Position restrained water wall
I'm not sure why it happens, but it might be a entropic effect: it is favorable to bind the already immobilized waters to the protein instead of water that could normally "be free". With the current setup I can't think of a way to fix this.

What I could think of is, instead of using polarizable water for you 'wall', use simple LJ-particles (you could say 'normal martini water') but change the C6-C12 parameters with respect to all other particles such that you get a purely repulsve particle. Thus, C12 would be zero and C6 would be some small value. A little trial and error might be needed to get this stable.

The same might be possible with the 'walls' implemented in Gromacs, but I have no experience with that.

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5 years 11 months ago #1719 by nanogod
Replied by nanogod on topic Position restrained water wall
Thank you for the reply djurre,

I have been experimenting with walls but belive that it may induce too many artifacts. That is why I was trying to use walls consisting of water. But propperly you are right, I properly need to use modiefed normal martini water and live with the influence it may have on the outcome.

Excuse me for asking, but isnt the C12 responsible for the repulsive part of the LJ potential and the C6 for the attractive part? So that C6 would be zero and C12 a small value?

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5 years 11 months ago #1720 by djurre
Replied by djurre on topic Position restrained water wall
Sorry, you're totally right. Mixed that up in the previous post.

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5 years 11 months ago #1721 by nanogod
Replied by nanogod on topic Position restrained water wall
Hmm, what do you think I need to do with epsilon_r if I use normal martini water as wall and PW as solvent inside the box?

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5 years 11 months ago #1723 by djurre
Replied by djurre on topic Position restrained water wall
Stick to the epsilon_r for polarizable water. The wall is really not your solvent.

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