Tc-grps value

User discussions
1

GROMACS version:2022.2
GROMACS modification: No
I want to run MD simulation to predict Antigen-Antibody interaction (Protein-protein) in a PBS buffer of pH-7.4 and at 303 K temp. What modifications do I need to make in a standard mdp file. Here are the changes, I can come up with. Please let me know if I am mistaken.

**Parameter**            =     **Standard Value**      ->     **Modified Value**

tc-grps                  =   Protein Non-Protein       ->    Protein Protein
ref_t                    = 298     298                 ->     303 303
gen_temp                 = 298                         ->     303                     
annealing_temp           = 50 298 50 298               ->    50 303 50 303

Since I am new to MD/Gromacs, Please guide me if these modification are good enough to perform MD simulation for aforementioned conditions or Do I need to add more conditions?

Thanks

2

Use the “standard” settings with the temperature changed to 303. The annealing_temp does nothing here in the absence of other settings controlling this behavior. Defining Protein twice with both (1) trigger an error about overlapping groups and (2) is nonsensical because you haven’t coupled your solvent to any thermostat. Distinct protein chains do not necessitate their own groups. Stick with Protein Non-Protein for tc-grps.

3

Thank you so much. It helped me alot.