1. In preparing the MD simulation, an equilibration of about 100 ns is done. After building the pure lipid membrane from CHARMM-GUI, I have 6 equilibration.mdp files and one production.mdp file. Please which of these files do I edit to achieve the 100 ns equilibration? 2. Please how do I extract the last snapshot of the pure lipid bilayer after equilibration and use that to build my complex in GROMACS?
3. In building the complex, how do I orient the peptide above the membrane? 3. Do I use the peptide membrane tutorial from the GROMACS website for simulating the complex? I would be grateful for any assistance offered.
Dear Jehoshaphat Oppong Mensah,
when you build your system(membrane/membrane-protein/nanodisk/...) on CHARMM-GUI, probably you got folder gromacs. In folder gromacs you can find README file, where you can see how to do Minimization, Equilibration and Production steps using gromacs. In each .mdp file you can find dt and nsteps, to equilibrate/simulate 100ns
For example:
dt = 0.002 and nsteps = 500000, t = 0.002 * 500000 = 1000 ps =1ns
if you repeat it 100 times: 100 * 1ns = 100ns
The last .gro/output file gives you coordinate of your system after 100ns.
Thank you very much for your answer. Is there a particular procedure for running the peptide membrane in GROMACS using the CHARMM force field? The procedure on the GROMACS website uses GROMOCS 96 and involves a lot of procedures. Also it is for simulating a peptide inserted in the membrane. Do I use the protein-ligand complex tutorial for simulating the peptide when it is placed above the membrane?
Actually, if you install GROMACS on your computer, there at least you can find these forcefields().
1: OPLSAA
2: AMBER
3: CHARMM27
4: GROMOS96
You can build Protein/Membrane(Protein inserted in membrane) system on CHARMM-GUI, then simulate on gromacs(it has charmm forcefield).
Yersultan Arynbek If I want to simulate the peptide when it is outside the membrane instead being inserted in the membrane, can I use the protein-ligand tutorial by treating the peptide as a ligand?
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