I am constructing a protein based hydrogel, using collagen like peptides. I would like to know how many waters and proteins are needed to have the desired system concentration of 10% w/v in silico for both an atomistic and coarse grained iteration.
If i understood well you want 10% of your simulation box filled with water. So you could, for example, build one box filled only with the proteins, with for example 20nm. Then you build one box with 2nm full of water molecules. You can run short equilibration simulations to see if the box sizes maintain. Finally you merge the two structures and let the pressure coupling to remove the free space that emerges in this step. Probably you will have to try different assemblies of the proteins in the initial box to obtain final solvated structures as you wish.
Other way is make the calculations, you just need to know the volume of each water molecule and each protein, decide how many proteins you want and calculate the needed water molecules to obtain 10% of volume.
Hi Egipto,
Thank you for your answers.
I have indeed tried both methods, using amber16, I constructed a box of 15 nm with 4 small TIP3P boxes spaced out in the 'protein box'. I do also the nessecary calculations but I would like to be sure that the proteins are efficiently solvated.
If any other methods come to mind in time, please let me know.
Finally is there any good in silico validation techniques or analytical tools needed to verify that the system is 10% w/v?
I don't Know in Amber, i'm a GROMACS user. In GROMACS you have the SASA (Solvent Accessible Surface Area) tool that have the -tv (total volume) allowing you to have an approximation of the volume.
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