GROMACS version: 2021.3
GROMACS modification: No
Hi, I am trying to replicate some results from a paper. From this, they scale down the charges of the phosphate group in ATP by 0.6. So in the topology file, I changed the charges by a factor of 0.6 for the phosphate group. Is this the correct way to go about this?
Secondly, the paper doesn’t state it scaled the charges of the ions. Therefore using the gmx genion, I would not get the same no. of molecules in the system as the paper, as they used 30 ATPs, 30 Mg2+, 68 Na + and 8 cl-. This tells me that the ATP is seen as a 4- instead of 4 x 0.6? Why is that? also gromacs identifies the ATP as -72 charge after scaling.
Thanks