Ethanol Polarity
- abelessi
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6 years 5 months ago #7424
by abelessi
Ethanol Polarity was created by abelessi
Dear all,
I am interested in modeling how small molecules (ethanol) can disrupt lipid membranes. The effect in question relies on the polarity of ethanol molecules which can stabilize both the hydrophobic tails and hydrophilic heads of lipids in solution.
Does Martini have any implementation that can take such effects into account? I realize that the level of coarse-graining used in the Martini force-field doesn't allow for a detailed representation of ethanol molecules (i.e. it is a single polar bead) but the polar bead type doesn't discriminate between hydrophobicity/hydrophilicity.
Would it be feasible to model an ethanol molecule as a kind of 'Janus' particle composed of hydrophobic and hydrophilic halves? I have done some initial tests of such a "bi-phasic" ethanol molecule but would like some feedback from more experienced Martini users.
Any suggestions are very welcome.
Thanks,
Alexis
I am interested in modeling how small molecules (ethanol) can disrupt lipid membranes. The effect in question relies on the polarity of ethanol molecules which can stabilize both the hydrophobic tails and hydrophilic heads of lipids in solution.
Does Martini have any implementation that can take such effects into account? I realize that the level of coarse-graining used in the Martini force-field doesn't allow for a detailed representation of ethanol molecules (i.e. it is a single polar bead) but the polar bead type doesn't discriminate between hydrophobicity/hydrophilicity.
Would it be feasible to model an ethanol molecule as a kind of 'Janus' particle composed of hydrophobic and hydrophilic halves? I have done some initial tests of such a "bi-phasic" ethanol molecule but would like some feedback from more experienced Martini users.
Any suggestions are very welcome.
Thanks,
Alexis
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- riccardo
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6 years 5 months ago #7438
by riccardo
Replied by riccardo on topic Ethanol Polarity
I would not model ethanol with an hydrophilic and hydrophobic part in Martini as this means having an almost united atom model (3 non-hydrogen atoms to 2 "Martini beads") which goes way to far from the 4-atoms-to-1-bead mapping scheme employed in Martini.
You could definitely check the effect of ethanol vs octanol etc, see, for example:
pubs.acs.org/doi/abs/10.1021/jacs.6b11091
You could definitely check the effect of ethanol vs octanol etc, see, for example:
pubs.acs.org/doi/abs/10.1021/jacs.6b11091
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- hoseinarani
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5 years 5 months ago #7886
by hoseinarani
Replied by hoseinarani on topic Ethanol Polarity
Dear,
I have an issue for modeling Ethanol+Lipid using CG modeling. I am modeling self-assembly of lipids (DPPC) in Water. However, the lipids are initially solved in alcohol (Ethanol) and then are mixed with water to form a bilayer. I used Martini CG simulation of lipid (DPPC) and ethanol. Lipids were randomly placed in an ethanol solvent (P2 type) simulation box. However, the NPT simulation showed that lipid aggregated to micelle which is not probable in pure alcohol. So, do you have any suggestion to make a good modeling of the system (Ethanol +Lipid) by which lipid be soluble in ethanol? Also, is it possible to modify Martini topology file and model ethanol as two separate bead spheres (each of which has less than 4 atoms)?
Thank you,
Hossein
I have an issue for modeling Ethanol+Lipid using CG modeling. I am modeling self-assembly of lipids (DPPC) in Water. However, the lipids are initially solved in alcohol (Ethanol) and then are mixed with water to form a bilayer. I used Martini CG simulation of lipid (DPPC) and ethanol. Lipids were randomly placed in an ethanol solvent (P2 type) simulation box. However, the NPT simulation showed that lipid aggregated to micelle which is not probable in pure alcohol. So, do you have any suggestion to make a good modeling of the system (Ethanol +Lipid) by which lipid be soluble in ethanol? Also, is it possible to modify Martini topology file and model ethanol as two separate bead spheres (each of which has less than 4 atoms)?
Thank you,
Hossein
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- jbarnoud
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5 years 5 months ago #7897
by jbarnoud
Replied by jbarnoud on topic Ethanol Polarity
As Riccardo wrote above, I would not represent ethanol with more than one martini bead. If you need to have 1.5 non-hydrogen atom per bead, maybe Martini does not have enough chemical resolution for your problem.
Regarding the micelles, what lipid are you using and what is the concentration? At high concentration of lipids, I would not be surprised to see micelles.
Regarding the micelles, what lipid are you using and what is the concentration? At high concentration of lipids, I would not be surprised to see micelles.
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- hoseinarani
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5 years 5 months ago #7898
by hoseinarani
Replied by hoseinarani on topic Ethanol Polarity
The system included DPPC, DPPG, Cholesterol, and Ethanol. The number of molecules is 50, 12, 50, and 475,000 respectively. The molecules were randomly placed in a simulation box. The simulation went through a self-assembly of DDPC+DPPG+CHOL which resulted in several Micelles. We did not see this event in an experiment.
I was thinking of creating a new ethanol molecule comprises two parts: polar and non-polar using SP2 and SC2 particle types. Attaching these two particles with a regular bond (bond length (0.47 nm) and force constant of K = 1250). What do you think? Any suggestion?
Thank you,
I was thinking of creating a new ethanol molecule comprises two parts: polar and non-polar using SP2 and SC2 particle types. Attaching these two particles with a regular bond (bond length (0.47 nm) and force constant of K = 1250). What do you think? Any suggestion?
Thank you,
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5 years 5 months ago #7899
by jbarnoud
Replied by jbarnoud on topic Ethanol Polarity
Did you try the same self assembly in water? Do you have micelles then?
You can build the solvent you describe, but it will be a stretch to call it ethanol.
You can build the solvent you describe, but it will be a stretch to call it ethanol.
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- hoseinarani
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5 years 5 months ago #7900
by hoseinarani
Replied by hoseinarani on topic Ethanol Polarity
Yes, I tested the same system in water (P4) and it formed micelles.
Do you have any idea to build ethanol molecule with associated parameters? Any tool, method, or tutorial for it?
Thank you,
Do you have any idea to build ethanol molecule with associated parameters? Any tool, method, or tutorial for it?
Thank you,
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- riccardo
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5 years 5 months ago #7901
by riccardo
Replied by riccardo on topic Ethanol Polarity
Let me re-state what Jonathan wrote. If you make up a Martini molecule with an SC2 and SP2 bead, you are describing a *at least* 4 heavy atom molecule but I would argue more like a *6 heavy atom* molecule composed of an hydrophilic and a hydrophobic part, so something like *pentanol*. So, if you want, you can do that, but I would indeed underline what Jonathan said: you can't call that ethanol. This is because the beads have been created to represent group of atoms of a certain size, namely 4 in the case of normal beads and 2-3 (better stick to the 3 side) in the case of the small beads (S-beads).
Continuing along the lines of building this pentanol, I would guess that a 0.47 nm bond is too long for such a molecule, since 0.47 nm is a typical bond length between consecutive beads in a 4-to-1 mapped alkyl chain. The proper way to do this would be to simulate at the atomistic level pentanol and then extract the distance between the center of mass of the two moieties of the molecule mapped into two beads. Probably you get something around 0.35 nm. The force constant then would be derived by matching the distribution of this distance along a trajectory at the CG and AA level. This is explained and shown in several tutorials and papers employing Martini.
Continuing along the lines of building this pentanol, I would guess that a 0.47 nm bond is too long for such a molecule, since 0.47 nm is a typical bond length between consecutive beads in a 4-to-1 mapped alkyl chain. The proper way to do this would be to simulate at the atomistic level pentanol and then extract the distance between the center of mass of the two moieties of the molecule mapped into two beads. Probably you get something around 0.35 nm. The force constant then would be derived by matching the distribution of this distance along a trajectory at the CG and AA level. This is explained and shown in several tutorials and papers employing Martini.
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- hoseinarani
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5 years 5 months ago #7903
by hoseinarani
Replied by hoseinarani on topic Ethanol Polarity
Thanks for the clarification. These would be helpful.
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5 years 5 months ago #7908
by jbarnoud
Replied by jbarnoud on topic Ethanol Polarity
As a side note. It may be that you observe micelles because of the low concentration of lipids in your box, rather than because of the solvent. As long as you do not get a bilayer in water there is likely something wrong in your system.
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