GROMACS version: 2022.4
GROMACS modification: No
I am trying to see if it is possible to simulate Tris-HCl buffer along with my protein to compare with some experimental results and check the buffer effect. But I am having difficulties. Do you have any suggestions how can i do this? or if it is possible?
Have you tried using gmx insert-molecules?
Buffers are generally present at such low concentrations that they would barely even be represented in a typical MD simulation box. Moreover, unless you are doing constant-pH MD simulations, the fact that the topologies are static (cannot dynamically change protonation state), it means you aren’t going to model their real chemical properties.
experimentally there were differences between the buffers and i am trying to simulate the protein in both buffers: sodium phosphate and Tris-HCl in order to compare the effect. If that makes sense.
I managed with Tris-HCl using the gmx-insert molecules, but i cannot get it right for the Na-P. Do you have any suggestions?
yes. it worked! thank youu!
What does this mean? The process of adding any arbitrary small molecules/buffers is the same. If it worked for Tris, it should work for phosphate (add Na+ with genion).