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How to differenciate Decane and Dodecane with the Martini force field
- Stéfane
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11 years 1 month ago #1412
by Stéfane
How to differenciate Decane and Dodecane with the Martini force field was created by Stéfane
Hello,
I am a new user of the Martini force field. I am trying to simulate a box of pure decane (256 mol). I have two questions about Martini.
Since in the force field
- A bead represent is 4 -> 1
- that in the martini_"v2.0_solvents.itp file" it is stated that the DECANE has the same topology as dodecane mol modeled both with 3 beads (C1 with the same mass).
It is not clear to me how I can differentiate the properties of these two molecules (e.g by their densities)
Additionally Can i change of the mass of each bead the mass of dodecane/3 in the itp file instead of the default mass for C1 ?
Thank you in advance
Stephane
I am a new user of the Martini force field. I am trying to simulate a box of pure decane (256 mol). I have two questions about Martini.
Since in the force field
- A bead represent is 4 -> 1
- that in the martini_"v2.0_solvents.itp file" it is stated that the DECANE has the same topology as dodecane mol modeled both with 3 beads (C1 with the same mass).
It is not clear to me how I can differentiate the properties of these two molecules (e.g by their densities)
Additionally Can i change of the mass of each bead the mass of dodecane/3 in the itp file instead of the default mass for C1 ?
Thank you in advance
Stephane
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- xavier
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11 years 1 month ago #1442
by xavier
Replied by xavier on topic How to differenciate Decane and Dodecane with the Martini force field
As you notice the difference between the decane and dodecane is not straightforward. The same goes with all the molecule chains that do not have a multiple of 4 heavy atoms. Then one needs to make choices. There is no rule that is followed but changing the masse in the analyses will give you the right density.
We also have thought of modifying the distance between beads. changing the polarity might also be solution. But as I said there is no systematic work and choices that have been made so far in the official martini release.
Let us know if you do something in that direction and wish to share.
We also have thought of modifying the distance between beads. changing the polarity might also be solution. But as I said there is no systematic work and choices that have been made so far in the official martini release.
Let us know if you do something in that direction and wish to share.
Stéfane wrote: Hello,
I am a new user of the Martini force field. I am trying to simulate a box of pure decane (256 mol). I have two questions about Martini.
Since in the force field
- A bead represent is 4 -> 1
- that in the martini_"v2.0_solvents.itp file" it is stated that the DECANE has the same topology as dodecane mol modeled both with 3 beads (C1 with the same mass).
It is not clear to me how I can differentiate the properties of these two molecules (e.g by their densities)
Additionally Can i change of the mass of each bead the mass of dodecane/3 in the itp file instead of the default mass for C1 ?
Thank you in advance
Stephane
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11 years 1 month ago #1443
by Stéfane
Replied by Stéfane on topic How to differenciate Decane and Dodecane with the Martini force field
OK thank you for your response, Xavier
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