Need help on NVT equilibration for MD simulation of Protein-RNA complex

[biosar...@gmail.com]

Respected All,

I am new to MD simulations. I am still learning Gromacs from tutorials and documentation.

I want to run MD simulation of protein (1700 amino acids) with ssRNA (around 80 nucleotides) and another dsRNA/dsDNA (around 20-40 nucleotides).

I am trying to understand how protein of interest interacts with dsDNA/dsRNA/ssDNA/ssRNA. what will be the difference in interactions when it interacts with different dsDNA/dsRNA/ssDNA/ssRNA and mutational studies on both protein and dsDNA/dsRNA/ssDNA/ssRNA.

And I am stuck with parameters in ‘initial phase’ NVT equilibration using Langevin bath which I have found from literature.

I am struggling to find the exact parameters for the protein-DNA/RNA system to run the three steps of the initial phase: (a) 10ps with increasing temperature from 0 to 100 K keeping protein & RNA fixed, (b) 25ps with temperature was further increased upto 200 K keeping backbone atoms of protein & RNA fixed and (c) 25ps to reach 298 K. Then NPT equilibration for 100 ps at 298 K

After this initial phase, NPT equilibration for 40-50ns followed by production run in microseconds.

I am not sure how to set parameters for MDP files for the three steps of the initial phase and NPT equilibration . I have googled it for few days, but not of much help. I end up with mdp files for free energy analysis only.

Why the NVT equilbration or initial phase is done with three steps in Langevin bath?

Why long runs for NPT equilibration?

Is it really necessary to do production run in microseconds?

I request you all to provide me the ‘mdp’ files for NVT and NPT equilibration as well as MD production to run the molecular dynamics simulations of protein/RNA complex.

I would be really thankful for your kind help.

Sorry for inconvenience, if any.

With Warm Regards,

Saravanan Parameswaran

PostDoctoral Fellow

Gyeongsang National University,

South Korea