Greetings,
I am performing a steered molecular dynamic simulation by pulling the R8 (Arginine) peptide via the constant velocity pulling method from the upper layer to the lower layer of the membrane having the following composition: DOPC/DOPG (4:1). During peptide translocation, some of the lipid molecules of the lower layer move out of the simulation box and start appearing at the upper layer. Can anyone please provide me with the lipid-centering script so that I can center the drifting lipids in the same simulation cell? In this SMD simulation, I have used the distance between the COM of P (Phosphorous) atoms of the upper layer and the COM of CA (C-alpha) atoms of the peptide as a reaction coordinate. For reference, I have attached the snapshots of my simulation system. Thank you
I look forward to receiving expert responses.
Note: Pulling a peptide along the negative Z direction
Kind regards,
Muhammad Raza
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