GROMACS version: 5.4.0
I used ParmEd package from gromacs to export the system set in the AMBER. The results from the gromacs simulation run contradicts to the simulation that run in the AMBER system.
What is the realiability of conversion using ParmED package?
I work on Protein-DNA system and so i use amber for initial system set up of interaction force field parameter (ParmBSC1 and ff14SB)
Been a while since I did anything with ParmED but its conversions were always faithful in my hands. You should check the single-point energy and forces in AMBER and GROMACS to make sure the topology and force field parameters are really the same.
Thanks for the suggestion. We double checked that the topology and force field parameters are same. The question raised only when the DNA parameters were studied with respect to time. The fluctuation in the gromacs system affects the overall average of the DNA parameters whereas the fluctaution not significant in the AMBER system .
By “DNA parameters” do you mean helicoidal parameters? How different were the outcomes? What was the time scale of the simulations and are the results reproducible in multiple, independent simulations? Are all the other algorithms, cutoff scheme, etc. identical between the two programs?
The simulation setups were checked and identical between two system. Time scale of the simulation run is 300 ns each. The values of gromacs is approximately three fold greater than AMBER affecting the overall average value of the base pair.
Values of what? I’m still not clear on what validation you did. Do you get matching forces and energies for a single frame?