normal Water Freezeing

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1 year 6 months ago #8550 by msajib
Water Freezeing was created by msajib
My system contains a big nanoparticle (10nm diameter) which we are keeping fixed throughout the simulation and multiple proteins, water. After assembling the desired system, I minimized the energy and trying to run NVT at 300K.

The problem is my water is freezing at about 5 ns. Even when I replace 10% of my standard CG water with antifreeze particles, it doesn't help.

Will polarizable water model help? Is there any other way I can solve this problem?

Thanks.

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1 year 6 months ago #8552 by vainikka
Replied by vainikka on topic Water Freezeing
Hi,

Sounds like an issue you get when a very large section of your system is constrained. You can try to lower the force constants on your position restraints.

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1 year 6 months ago #8554 by msajib
Replied by msajib on topic Water Freezeing
Thanks.

I am actually fixing my nanoparticle atoms by directly applying freezegrps and freezedims command of gromacs as I listed below. Is this approach wrong for martini to fix the atom?

freezegrps = Nanoparticle
freezedim = Y Y Y


If I correctly understand you, I should generate a position restrains file (posre.itp) for my Nanoparticle atoms, lower their force constant and then use that in my mdp file as

define = -DPOSRES

Did I get that correctly?

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1 year 6 months ago #8555 by vainikka
Replied by vainikka on topic Water Freezeing
Hi,

Yes, you can create an additional .itp file for the restraints, of append your existing .itp file. The GROMACS reference manual section 4.3.1 and table 5.5 should have all the information you require.

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1 year 6 months ago #8557 by msajib
Replied by msajib on topic Water Freezeing
Thanks a lot for the direction.

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