I have been running a membrane protein simulation. I followed the tutorial on: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
But I faced a problem in the shrinking phase. I have done up to 14 cycles of the shrinking phase using inflate gro. I got only 2.14513126335007 nm^2 area per lipid. The protein was in the membrane up to 13 cycles but after the 14th cycle it came away from the lipid bilayer. I was unable to find the error. Please help me in this regard.
Hello.
Since GROMACS 4.5.4, you have an alternative method to insert protein in membranes: g_membed (Wolf, MG et al. J Comput Chem, 31(11), 2169–74. doi:10.1002/jcc.21507), and works a lot better.
Check the GROMACS manual, you'll find instructions. If you need further assistance, I can send to you more detailed instructions and the .mdp file.
Best Regards.
Hello.
Since GROMACS 4.5.4, you have an alternative method to insert protein in membranes: g_membed (Wolf, MG et al. J Comput Chem, 31(11), 2169–74. doi:10.1002/jcc.21507), and works a lot better.
Check the GROMACS manual, you'll find instructions. If you need further assistance, I can send to you more detailed instructions and the .mdp file.
Best Regards.
Hello.
Here you have the membed.mdp file for membrane insertion.
Instructions:
1) Join the protein.gro and membrane.gro in one file: cat membrane.gro >> protein.gro;
2) Correct the topology file (to include FF for both protein and lipid).
3) Follow manual instructions (or in the original publication): they have all you need.
Best regards.
Hello.
No, that file is to generate the .tpr file to be used in g_membed. You have to manually merge the two files.
Best regards.
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