Dear Researchers!
I have one query regarding SMD (Steered Molecular Dynamics) method implementation in the NAMD package; please address it if anyone knows the answer. Please note that I'm working on the interaction of CPPs(Arginine Peptide) with the model membrane.
My Question: Literature shows that in the SMD, one should apply the harmonic potential with some specific force constant (let's say 1000 kJ per mol) value between the COM(center of mass) of the peptide and one reference point determined with respect to the COM of the lipid bilayer. Here, my point is how I can specify or calculate the COM of peptide and lipid bilayer to use them for the SMD method. I mean, are there any specific commands for using them? I get the following parameters? Thank in advance
Kind regards,
Muhammad Raza
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