Hi Friends,
I have done a molecular dynamics simulation of a DNA molecule for 100ns in Gromacs with amber force field. I expected a well stabilized system but I got structures with small disruptions during the simulation. I want to know that without disturbing the DNA molecule (counter ions added, normal pressure & temperature and no ligand added) how the structure has some modifications? I herewith attached the files for your reference.
With regards,
R. Radhika
How did you assemble your DNA? Check the in silico details. Where are the files?
I have extracted the DNA from protein data bank. It was complexed with cisplatin. The files are got during the simulation for each 10ns.
Hi Geethu, as i suspected it looks like an imaging problem. See the following post and that should help correct the structure.
https://www.researchgate.net/post/How_can_I_deal_with_the_substrate_moving_out_of_the_box_during_MD_simulation
Dear Dr. Senthil,
Thank you so much for the suggestion. I will try to do that.
Dear Dr. Senthil,
Thank you so much for the suggestion. The link was so useful. Using the wrap command we can change the image but what about the analyses? If I do the MD analyses again what should I do to include the wrapped structure in the trajectory?
Try to remove the drift and the rotation of the DNA molecule and of the solvent before to start the MD simulations.
Thanks for the suggestion friends. I got the correct structure by the removal of periodic boundary conditions.
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