Ok, Thanks for your reply,sir.
The system should be fully neutralized. Since insane is supposed to do that for you, you will need to check why the charges in your itp files do not seem to agree with the charges of the same molecule types in insane.
You can of course add two sodium ions to neutralize the system, but I think it’s better for you if you try to find the root of the problem.
Ok, Thanks for your reply and suggestion,sir.
I keep encountering an “infinite total potential energy” error during the minimization step of my Go Martini simulation for the serotonin receptor, using the 10 ns equilibrated structure from CHARMM-GUI. Previously, I didn’t get this error, when i performed simulation.
I’ve tried running the simulation multiple times and adjusted parameters like emtol and nsteps, but nothing seems to resolve the issue. I’ve attached the complete command line outputs and the minimization.mdp file I used.
Could you provide some suggestions on how to address this error?
Thank you!
mderror.txt (298.4 KB)
minimization.mdp.txt (4.6 KB)
As I’ve said before, you should first see why you get a system net charge of -649 after insane has added ions to neutralize the system. Your force field does not seem to match the components that insane uses. You might be using wrong itp files for you system components.
Apart from that you should check atoms 21431 and 21432 and everything within, e.g., 3 Å from them.
Ok, sir. Thanks for your prompt response.
I’m confused by the SAPX molecules. In insane you specify the numbers of SAP3, SAP5 and SAP6. In the index file the groups are called SAP3, SAP5 and SAP6. But in the grompp output it says:
Excluding 1 bonded neighbours molecule type 'SAP1_5'
Excluding 1 bonded neighbours molecule type 'SAP2_45'
Excluding 1 bonded neighbours molecule type 'SAP3_345'
Are these correct?
Hi, Sir
Because SAPX (Pip lipids) molecules have different names in the Phosphoinositide itp file and insane script. Thus, I manually changed sap3 to sap1_5 in the topology file after the insane step.
As soon as I can, I will check all the atoms in my structure are within 3A and find a solution to the charge issue. Strangely, I ran the up to minimization step last time using the same structure. So that’s why I messaged you. Why can’t I run again now?
I will get back to you soon, once I have done that.
In the insane.py script there are these lines:
# Lists for automatic charge determination
charges = {"ARG":1, "LYS":1, "ASP":-1, "GLU":-1, "DOPG":-1, "POPG":-1, "DOPS":-1, "POPS":-1, "DSSQ":-1}
You need to go through all the molecule types you are using and add the charged ones, otherwise insane cannot neutralize your system correctly. You could also skip neutralizing your system with insane and just do it using GROMACS tools. Trying/having to do both is an indication that something is not going according to plan.
Okay. Thanks for your comments. I’ll take a look at them.
Thank you so much for your help, sir.
Once again, add the ions with INSANE or gmx genion. I don’t think you should need both.
You said that the system total charge was -2 (presumably from the protein, right?), but gmx genion is apparently trying to add 42 Na+ ions (indicating that the system has a -40 charge). Are you using the correct tpr as input? Why are you using both the option -neutral and -np 2? That means that you will neutralize the system and add two more sodium ions. Then you will have a net charge of +2.
I’m afraid I can’t help you with any specific NaCl-water solvent. If that is suggested in a tutorial, then I guess you can try it.
Ok, sir.
Thanks for your comments. I will try and let you know the outcome soon.
Hi, Sir
I manually added two Na+ ions to neutralize the system and performed a 30 ns simulation. However, after the simulation, I noticed that the membrane is no longer flat—it appears constricted at one end, and the protein has become hided within the membrane. This behavior was not observed after the equilibration phase. Could you please suggest why this change might have occurred? Is this outcome acceptable?
I’ve attached images from before and after the simulation for your reference.
Good that you got the simulations up and running. I’m afraid I can’t give any specific advice on your system, since I don’t know anything about it. I guess you are running the equilibrations with position restraints, so it’s no wonder that these problems (if any) didn’t show up then. The first thing I would try is to equilibrate longer to see if that helps. Otherwise, I guess it might be a system setup problem, or a force field issue.
Thanks for your prompt reply, sir.
I have another doubt. The ITP file for ceramide is available, but the ceramide lipid is not included in the insane script. Can you suggest how to add this lipid to the insane script? Is it challenging to incorporate a new lipid into the insane script?
Does this help GitHub - Martini-Force-Field-Initiative/M3-Sterol-Parameters: Home of the Martini 3 Sterol Parameters.?
Thanks for the reply, I will check it, sir