[gmx-users] DNA simulation and choice of temperature coupling groups

[Athina Meletiou]

Hello all,

I was looking into performing some MD simulations of a DNA molecule - as a control to simulations of the same DNA molecule along with its binding protein. However I’m getting a bit confused about how to use temperature coupling groups. I am torn between simply using one group (“System”) or two groups (“DNA” and “Water_and_ions”). I’m leaning towards a single group (“System”) and that’s because 1) the groups I have used for the DNA and binding protein simulations were “Protein” and “Non-protein”, meaning that in those my DNA molecule was grouped together with the solvent and ions. Therefore for comparability I’m thinking that using “System” for the DNA simulations may be best. Also 2) using one group for the solute (DNA) and another for the solvent (Water_and_ions) can introduce artifacts into the conformational dynamics of my DNA molecule.

I would appreciate any insights/hints, thank you all in advance.

Kind regards,
Athina




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