GROMACS version: 2020.1
GROMACS modification: Yes/No
Dear members of the community, I am a beginner in this field. I would like to simulate my protein (a mitotic kinesin) in the presence of 8M urea. I have finished the tutorial “Lysozyme in water” and I am somewhat acquainted with the workflow of Gromacs. I am just starting from scratch. Can anyone please help me in sharing the exact step-by-step process of how to do the simulation of protein in 8 M urea. Many thanks in advance.
Hi, respected community members. My last post did not get much attention; however, I tried to simulate my protein of interest in a mixture of urea and water. I am however stuck in the very first step. How can I calculate the concentration 8 M Urea in an MD simulation. My protein is placed in a cubic box with dimensions:
new center : 2.654 2.654 2.654 (nm)
new box vectors : 5.307 5.307 5.307 (nm)
I also tried to check how many water molecules are actually added in this box by gromacs by using the solvate command and I found out that the number is 4621 solvent molecules.
Now, how many molecules of urea are to be added in this box so as to get a concentration of 8M.
Please help me out in this calculation. Thanks.
https://www.gromacs.org/Documentation_of_outdated_versions/How-tos/Mixed_Solvents
To calculate concentration, refer to any basic chemistry textbook.