normal Question about the charge and mass of beads.

  • 若水无风
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2 years 9 months ago #8979 by 若水无风
Question about the charge and mass of beads. was created by 若水无风
I am learning how to use the Martini by following the the tutorials of polymer. I want to know whether it is necessary to assign the charge and mass of the molecules to the corresponding beads. Because when i use the default bead mass and size ,it is hard to reproduce the density of AA simulation, also the free-energy of PEG in water (about 120 kJ/mol) deviates from the results of molecular simulations (about 7 kJ/mol). If there any methods to modify the relevant parameters to solve the problem?
Grateful for your advise,sincerely.

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2 years 9 months ago #8995 by riccardo
Replied by riccardo on topic Question about the charge and mass of beads.
Unless there's a group of atoms carries a charge (e.g., a charged lipid head), in standard Martini there are no charges on the beads.

We also use standard masses. If you want to extract densities directly from gromacs, though, you should take care of that (see, e.g., here: cgmartini.nl/index.php/component/kunena/...2384-benzene-density ).

Not sure what you mean by "free-energy of PEG in water". Which kind of free energy are you interested in computing?

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2 years 9 months ago #9018 by 若水无风
Replied by 若水无风 on topic Question about the charge and mass of beads.
Thanks for your reply. The question about bead's charge was arise from the too large free-energy of PEG in water, whether bead charge have some effects on the calculation of free energy?

I just following the tutorials of polymer to learn how to use Martini, "free-energy of PEG in water" is computed to verify the melt-water partition of CG model that i build.

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2 years 9 months ago - 2 years 9 months ago #9019 by riccardo
Replied by riccardo on topic Question about the charge and mass of beads.
Ok, i understand you are computing the free energy of transfer, or partitioning free energy, of PEG (how many repeat units?) between water and a PEG melt - is that so?

Yes, charges will have an impact on the calculation of such a free energy. If you for example use charges on PEG and/or water, then this will change the free energy computed with respect to the value computed when no charged beads are used.

Note that PEG and water both carry no charge in standard (i.e., non-polarizable) Martini.
Last edit: 2 years 9 months ago by riccardo.

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2 years 9 months ago #9023 by 若水无风
Replied by 若水无风 on topic Question about the charge and mass of beads.
Yes.There are 10 repeat units in one PEG molecule, as the AA simulation results provided.

When i check the free energy compute results of PEG melt or PEG in water that the tutorial peovided, i find both Coulomb and VdWaals interaction contribute to the free energy. However there is no charge in the system. Given the polarity of the water, whether is it possible that the water polarized the PEG and how much does polarization affect the free energy? Standard Martini bead with no charge doesn't consider the polarization?

Thanks a lot for your reply.

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2 years 9 months ago #9039 by hind
Dear All,

Is histidine in the form of HSP available in martini CG? If not, could you please suggest how to get it?

Thanks

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2 years 9 months ago #9045 by riccardo
Replied by riccardo on topic Question about the charge and mass of beads.
@若水无风: standard Martini beads (incl. standard Martini water) have no charge so there can't be Coulomb interactions (nor any other polarization effect if by that you mean anything involving charges). The polarity of water is captured "effectively" by a parameterized Lennard-Jones potential in standard Martini water.

@hind: please, open a separate thread in the forum for questions not related to the topic of the thread. (Also, what does HSP mean?)

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2 years 9 months ago #9049 by 若水无风
Replied by 若水无风 on topic Question about the charge and mass of beads.
Thank you very much for your patience in answering my questions!

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