normal Charged beads

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2 years 3 months ago #9353 by GhazalehYA
Charged beads was created by GhazalehYA
Hello,
I did MD simulation n the gas phase for hairpin RNA with all negative charges on prophase groups for all-atom model, result showed that all charged repelled each other and open the hairpin. On the other hand, when I ran MD for the same hairpin RNA in the gas phase for coarse-grained model, I did not observed any changes in structure.
Can you please explain how charges interact in the coarse-grained model?

Best,
Gazelle

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2 years 2 months ago #9358 by riccardo
Replied by riccardo on topic Charged beads
This kind of conformational changes cannot be described with Martini because you usually apply an elastic network to keep RNA's (or DNA's or proteins') structure close to a reference structure. Hence, with (default) Martini models you can't observe RNA hairpin opening. Be sure to thoroughly go through the Martini RNA ( doi.org/10.1016/j.bpj.2017.05.043 ) and DNA: pubs.acs.org/doi/pdf/10.1021/acs.jctc.5b00286 ) papers.

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2 years 2 months ago #9361 by GhazalehYA
Replied by GhazalehYA on topic Charged beads
Dear Riccardo,

Thank you for the info!

Your answer made me reconsider the whole process, looking for things that I might be missing.
a) I started from an all-atom *.pdb and created a CG *.pdb using the martinize-nucleotide.py. The process generated also the corresponding *.itp and *.top files.
b) Next, we ran the sed process to include the martini.itp files (different version). The process generated a new *.top file.
c) At this point, we ran the gmx grompp process to create the *.tpr file input for energy minimization.
d) We ran the mdrun process by using the input *.tpr file.
e) We finally ran the MD simulation.

Based on these steps, my understanding is that GROMACS is running minimization and simulation on inputs generated by martini.

When I run minimization and simulation in all-atom mode with no water or counterions (what we call gas phase), GROMACS demonstrated to be capable of handling the expected charge repulsion, as it showed that the hairpin opened up. The fact that now GROMACS cannot do this anymore when the inputs are created by martini is puzzling. If the charges are described properly in the inputs generated by martini, it should still be able to calculate the effects of charge repulsion.

Any suggestion will be greatly appreciated.

Best,

Gazelle

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