normal Topology file for decane

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11 years 15 hours ago #1495 by chenyuetian
Topology file for decane was created by chenyuetian
Dear all forum users,
I am using decane (molecular formula: C10H22) as the solvent molecules in my simulation with Martini FF. I noticed that the MARTINI developers applied decane as a CG solvent in J. Chem. Theory Comput. 2012, 8, 1003−1014, but I couldn't find neither the structure file of decane, nor the topology file of decane from the Martini's website. The website provides martini_v2.0_solvents.itp, but there is no specific topology for decane inside.
So could you please provide the topology file of decane to me, so that I can do the reverse transformation to get its CG structure from the FG structure? It will be more convenient to also get the structure file of decane in .gro/.pdb format directly from you (The structure file of benzene in .gro/.pdb format will also be useful to me). Thank you very much for your help.
Ps: If possible, could anyone add my e-mail address: This email address is being protected from spambots. You need JavaScript enabled to view it. to the Martini Mailing List?
Best regards,

Yuwu

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10 years 11 months ago #1496 by djurre
Replied by djurre on topic Topology file for decane
Since Martini is a Coarse Grain force field with a 4:1 mapping, not every molecule can be uniquely mapped. For linear alkanes this means that several alkanes have the same mapping. As you can see in the original martini paper (dx.doi.org/10.1021/jp036508g), table 2 Decane and dodecane have the same number of beads (3). This is also mentioned in the martini_v2.0_solvents.itp.

Creating stucture files can be easily done by hand: Just create or edit a gro file in a text editor. Decane are three beads in a linear conformation, benzene in a triangular. Once you have one molecule you can multiply it using genconf (a Gromacs tool) and quickly relax it by simulating it for 10-50 ns. That the magic of Coarse Grain!

There is no Martini mailing list. There is the forum. I did see your question there, but did not have time to answer it yet.

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10 years 11 months ago #1497 by chenyuetian
Replied by chenyuetian on topic Topology file for decane
Thank you so much for your informative reply.
Can I understand that instead of the transformation from the FG representation, which means install a modified GROMACS 3.3.1 and many SA runs, now what I need to do is to build the CG sturcture files directly, following the procedure in your reply? If so, any suggestions about the initial distance between the beads in one molecule? And what are the energy minimization, NVT and NPT equilibrium time, respectively? I agree that 10-50 ns for a system with just some alkane molecules is a quickly relax time in Martini simulation.

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10 years 11 months ago #1498 by djurre
Replied by djurre on topic Topology file for decane
If you are not looking for any specific starting structure (for example specific lipids/peptides binding to a protein) you don't need a reverse transformation. Just start from a random configuration and sample long enough that your system is in equilibrium.
For the initial distances in you structure file I would use the equilibrium distances in the itp file. The EM, NPT and NVT times depend you system.

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10 years 11 months ago #1499 by chenyuetian
Replied by chenyuetian on topic Topology file for decane
Thanks!

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