Muhammad Raza

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Questions related from Muhammad Raza

Lipids are moving out of the simulation cell during SMD Simulation (Constant Velocity)?

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...

05 December 2023 590 0 View

How To Constraint the COM(center of mass) of lipid bilayer in SMD simulation on NAMD?

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...

05 January 2023 6,021 0 View

How to extract CA-atoms and P-atoms information from large dcd file? and, how to read a DCD file in MATLAB?

Greetings, I am working on MD simulations, specifically on CPPs and cell-membrane interaction. Can anyone please guide me on how I can extract the CA-atoms and P-atoms (Phosphorus atoms of the...

03 October 2022 9,081 0 View