normal martini_v2.1-dna.itp vs martini_v2.0.itp

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2 years 4 months ago #9313 by Guruge
Dear Experts,

My system contains RNA and some lipid molecules. I got the RNA topologies using the martinize-nucleotide.py. From the .top file I got from python script includes martini_v2.1-dna.itp. However, I noticed that martini_v2.1-dna.itp contains different non-bonded parameters for beads compared to martini_v2.0.itp. For example,

P5 P5 1 0.24145E-00 0.26027E-02 (martini_v2.0.itp)

P5 P5 1 4.700000e-01 5.600000e+00 (martini_v2.1-dna.itp)

May I know why non-bonded parameters are different in two itp files? Appreciate, if you could answer my question.

Thank you.

Best regards
Guruge

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2 years 4 months ago - 2 years 4 months ago #9314 by riccardo
Replied by riccardo on topic martini_v2.1-dna.itp vs martini_v2.0.itp
Those lines are equivalent. In the first line, the 2 parameters are the Lennard-Jones C6 and C12 and in the second line they are the Lennard-Jones sigma and epsilon. You can check that they are equivalent with, for example, the gromacs tool "gmx sigeps", namely, try running:

gmx sigeps -sig 4.700000e-01 -eps 5.600000e+00
Last edit: 2 years 4 months ago by riccardo.

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2 years 4 months ago #9315 by Guruge
Replied by Guruge on topic martini_v2.1-dna.itp vs martini_v2.0.itp
Dear Prof. Riccardo,

Thank you so much for the reply. Now I got it.

Cheers!

Best Regards
Guruge

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2 years 4 months ago #9316 by Guruge
Replied by Guruge on topic martini_v2.1-dna.itp vs martini_v2.0.itp
Dear Prof. Riccardo,

I have one more thing to ask. My system contains RNA with polyethylene oxide molecules. I want to combine parameters in martini_v2.0_PEO.itp and martini_v2.1-dna.itp. However, I cannot do that since one contain C6/C12 parameters (martini_v2.0_PEO.itp) while the other file contains sigma and epsilon values (martini_v2.1-dna.itp). Therefore, where can I find martini_v2.0.itp file with C6 and C12 values instead of sigma and epsilon values (or other way around)?

Thank you.

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2 years 4 months ago #9317 by riccardo
Replied by riccardo on topic martini_v2.1-dna.itp vs martini_v2.0.itp
I would write a script that loops over the lines of the file you want to convert and, using gmx sigeps or your own implementation of the conversion, converts the c6/c12 to sig/eps or vice versa and prints them to a new file.

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2 years 3 months ago #9318 by Guruge
Replied by Guruge on topic martini_v2.1-dna.itp vs martini_v2.0.itp
Dear Prof. Riccardo,

Thank you very much for the answer.

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2 years 3 months ago - 2 years 3 months ago #9319 by Guruge
Replied by Guruge on topic martini_v2.1-dna.itp vs martini_v2.0.itp
Also, when I generate the topology for RNA using martinize-nucleotide.py, the topology file includes the statement; "This topology is based on development beta of Martini DNA and should NOT be used for production runs". What is the meaning of this? Can't I use the generated topology for MD simulations? Appreciate, if you could comment on this.

Thank you.
Last edit: 2 years 3 months ago by Guruge.

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