GROMACS version:2022
GROMACS modification: No
Dear all,
I performed a md simulation for a model which is constructed using CHARMM_GUI. After I finished NVT equilibration, I prepared to perform 100 ns NPT equilibration. Unfortunately, during the NPT equilibration, a sodium ion, which was only added after neturalizing the system, entered into the active region and bound with the substrate. It is very confusing because in the original crystal structure, there is no any sodium ion in the active site. In fact, it is not possible to happen, in my humble opinion.
If anyone has any advice on how to deal with this problem, it would be very appreciated. Thanks!
Hi,
my suggestion is not only to neutralize the system, but also to add ions to archive the desired concentrations. Then first to relax ions and water position with position restraints on the macromolecule.
see Introduction to Molecular Dynamics — GROMACS tutorials https://tutorials.gromacs.org documentation
I hope it helps.
Alessandra
1 Like
Hi Alevilla,
Thank you for your reply.
I also did them as you suggested. This is my restraint command: define = -DPOSRES -DPOSRES_FC_BB=400.0 -DPOSRES_FC_SC=40.0 ; However, the sodium ions also went in to the active region and bound with the subsrate when the NPT equilibration was running. It is very annoying. Should I restaint the sodium ions?
Best wishes,
Wenhao
I think chemically this could happen if your active site is full of negatively charged residues. You could run longer simulations and see how it goes. I think it’s very possible that some ion enter an active site and leave very shortly afterwards.
Hi,
Thanks for you reply. Yeah. I agree with you. However, the orginal crystal structure does not contain any sodium ion or potassium ion in the active site. It is very weird. And I want to add position restraints on sodium ions which are in the constructed water box during the NPT equilibration. Do you think I should or shouldn’t restrain the sodium ions?
Wenhao