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9 years 8 months ago #4012 by yipy0005
How to verify CG solvent properties? was created by yipy0005
Hi, I wish to ask if let's say I simulate a CG protein in a CG solvent with MARTINI, what thermodynamic properties of the CG solvent can I verify to make sure that the simulation is reasonably correct?

Thanks.

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9 years 8 months ago #4013 by xavier
Replied by xavier on topic How to verify CG solvent properties?
Hi, it always depends on what you want to know.

I do not know any thermodynamic properties of a solvent that one can measure to evaluate if a simulation of a protein is correct. It is probably because there are none! This is potentially true for all type of models.

You might want alternatively to look at the behaviour of the protein. Translational and rotational diffusion …

Note that the aqueous phase (water) in Martini is truly coarse grain and can not really be considered very realistic. It does give a relative good representation of the viscosity and partitioning but besides this it is pretty much a simple model. Notably it does not have any electrostatic properties … unless you used the polarisable version.

I hope this helps.

yipy0005 wrote: Hi, I wish to ask if let's say I simulate a CG protein in a CG solvent with MARTINI, what thermodynamic properties of the CG solvent can I verify to make sure that the simulation is reasonably correct?

Thanks.

Please Log in or Create an account to join the conversation.

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