[gmx-users] Need help on NVT equilibration for MD simulation of Protein-RNA complex

[Saravanan Parameswaran]

​​
​Dear Simulators,,

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.


With Warm Regards,

Saravanan Parameswaran

PostDoctoral Fellow

Gyeongsang National University,

South Korea