I am doing umbrella sampling with a very low speed but still some lipids are coming out with the protein .So is it possible to add position restraints on bilayers by GROMACS?
Hi Priyanka,
You may find this publication useful (available as PDF online):
Membrane protein tutorial with GROMACS - VI-SEEM Training Portal
https://training.vi-seem.eu/images/trainingMaterial/LifeSciences/memprot_tutorial.pdf
solvated lipid bilayer using the GROMACS program and its associated tools. The tutorial makes uses of ... Run the GROMACS pdb2gmx command to generate the protein topology and add the missing hydrogens to the protein, This program also takes ... posre.itp - a file with the position restraints. Make a file with the protein ...
Hi M.R. Mozafari,
Thank you so much for your suggestion.
The tutorial which you suggest me to follow in that they have used position restrain on protein.I have also used position restrain for protein in my simulation. But the problem is different. In my simulation , i want to do pulling of protein through the bilayers but after pulling the protein through the bilayer, some lipid follows the protein.
Hi Priyanka,
I think you can use position restraints for lipids by defining them in your topology file (or .itp files). However, suppressing the system's feature by applying some restraint should not be an appropriate way of doing. You should first find out that is it really an artifact or it is hinting some thing obvious which you are not considering in your assumption.
Thanks
Gourav Shrivastav
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