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normal CG/ Topology Toluene

  • panzu
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10 years 6 months ago #2248 by panzu
CG/ Topology Toluene was created by panzu
Dear all users,

I would like to use Toluene as a molecular solvent in a simulation but I couldn't find neither the structure file of toluene, nor the topology file of toluene from the Martini's website. The website provides martini_v2.0_solvents.itp, but there is no information about toluene inside.

I am wondering how I could get the Toluene.gro/pdb file and a martini_solvents.itp that contains information about its CG.
Any suggestion about making simulation with Toluene would be appreciated. Thanks in advance.

Best regards,

Sergio

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10 years 6 months ago - 10 years 6 months ago #2253 by Clement
Replied by Clement on topic CG/ Topology Toluene
As far as I know, there's no model for toluene. But it's a simple molecule, and the CG model should be fairly easy to derive from the benzene CG model. I don't think the topology would be too different from it; one bead would be a bit more hydrophobic (SC5 to SC3 or SC2 maybe). You could validate your model by testing it against experimental partition data (logP), according to the Martini philosophy.
Last edit: 10 years 6 months ago by Clement.

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10 years 6 months ago #2254 by panzu
Replied by panzu on topic CG/ Topology Toluene
Thank you very much!

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10 years 6 months ago #2261 by siewert
Replied by siewert on topic CG/ Topology Toluene
Note that we treat the phenylalanine aminoacid sidechain, which is essentially toluene, the same as benzene (three SC5 particles). This topology has been verified against, e.g., partitioning across the membrane (see the latest Martini 2.2 paper by de Jong et al, JCTC, 2013)

But it would indeed make sense to increase the hydrophobicity of one of the beads slightly to mimic the chemical nature of toluene more faithfully.

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10 years 6 months ago #2294 by panzu
Replied by panzu on topic CG/ Topology Toluene
Thank a lot again, I will try both methods.

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