GROMACS version:2022.5
GROMACS modification: No
Hi all,
I have done a protein-ligand-POPC membrane simulation for 100 ns in Gromacs. The protein-ligand-POPC bilayer were designed by using CHARMM-GUI. Charmm-GUI defined the position restrains for the protein using POSRES_FC_BB and POSRES_FC_SC (BB for backbones and SC for sidechains). For lipids, the position restrains were defined as POSRES_FC_LIPID. Interestingly, CHARMM GUI defined the position restrains for ligand also as POSRES_FC_BB (heavy atoms of ligand). Now while performing the NVT and NPT equilibration I performed 2 different NVT equilibration runs and 4 different NPT equilibration runs. In each run the position restrains were slowly decreased and removed eventually on the membrane while the position restrains were also reduced gradually in each step for protein and ligand since both of them were defined as POSRES_FC_BB. For the better understanding of the readers I am attaching the force constants for each step of equilibration below:
NVT 1 - define = -DPOSRES -DPOSRES_FC_BB=4000.0 -DPOSRES_FC_SC=2000.0 -DPOSRES_FC_LIPID=1000.0 -DDIHRES -DDIHRES_FC=1000.0
NVT 2 define = -DPOSRES -DPOSRES_FC_BB=2000.0 -DPOSRES_FC_SC=1000.0 -DPOSRES_FC_LIPID=400.0 -DDIHRES -DDIHRES_FC=400.0
NPT 1 define = -DPOSRES -DPOSRES_FC_BB=1000.0 -DPOSRES_FC_SC=500.0 -DPOSRES_FC_LIPID=400.0 -DDIHRES -DDIHRES_FC=200.0
NPT 2 define = -DPOSRES -DPOSRES_FC_BB=500.0 -DPOSRES_FC_SC=200.0 -DPOSRES_FC_LIPID=200.0 -DDIHRES -DDIHRES_FC=200.0
NPT 3 define = -DPOSRES -DPOSRES_FC_BB=200.0 -DPOSRES_FC_SC=50.0 -DPOSRES_FC_LIPID=40.0 -DDIHRES -DDIHRES_FC=100.0
NPT 4 define = -DPOSRES -DPOSRES_FC_BB=50.0 -DPOSRES_FC_SC=0.0 -DPOSRES_FC_LIPID=0.0 -DDIHRES -DDIHRES_FC=0.0
Now as I mentioned before, since the position restrains on the protein were relaxed, the restrains on ligand were also reduced eventually during this process. As a result of this the conformation of my ligand changed to a certain extent as compared to my initial input conformation after completing the equilibration runs.
I am attaching a picture of the initial structure of ligand (red color) and structure after NPT4 equilibration (Blue) for your reference.
Also, I checked, that there were no major changes in ligand conformation during energy minimization steps it happens only during equilibration steps. Now that being said, my question is that technically I am not starting my simulation with my initial ligand conformation hence will it be fine to consider this small yet evident change in conformation of the ligand during the equilibration phase or is it bad? .
I am new to this field so I need some insights from experienced members of the community. Kindly guide me.
Many thanks in advance.