GROMACS version:2020.6
GROMACS modification: Yes/No
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Can anyone suggest what should be a suitable forcefield for simulating IDP protein molecule like alpha synuclein with small molecules?
Is the AMBER99sb-ILDN forcefield a correct choice?
I would recommend CHARMM36m Newest CHARMM36 port for GROMACS - #41 by jalemkul
Actually I am using gromacs 2020.6 which has CHARMM27 all atom force field. Do you think it is a suitable choice?
It would be more suitable to use the more up-to-date CHARMM36. You don’t need a specific version for gromacs, if you take the folder containing the forcefield and make sure it’s in the same directory as the one you’re working in, it will show up as an option when you run pdb2gmx
Okay. Another thing I want to know is that if I use the charmm forcefield then do I need to generate the ligand parameter files like the itp file from charmm gui only or I can use some other server like acpype?
With CHARMM, you could either use charmm gui or CGENFF Protein-Ligand Complex , CGENFF might be more straightforward
Thank you very much. One more thing, how to make sure that the ligand is compatible with the forcefield I have chosen? I mean to say that suppose I generate the ligand parameters via CHARMM GUI and then I am doing the simulation in CHARMM36m forcefield so does it already imply that my ligand is compatible with the forcefield since the server that I have used to generate the ligand parameters is based on the same forcefield where I am doing the simulation?
Or is it required to check by some means that the ligand is fine with the forcefield?
See Is it allowed to use Charmm36 ff on protein and GAFF on ligand? - #2 by MagnusL . Typically for CHARMM you want to use CGENFF specifically. I recall charmmgui giving you a choice for which forcefields to use for the ligand but don’t remember which ones are available, but they likely set the correct one for you by default.
Thanks a lot. Actually I am a beginner with gromacs so some basic questions are cropping up.
Suppose I am calculating RDF of the ligand with respect to different regions of the protein molecule. Then is it required to do the calculation with respect to the center of mass of coordinates or I can do without considering the centre of mass? Which one is more suitable?
You would need to calculate it with respect to some reference point no matter what (see gmx rdf - GROMACS 2026.2 documentation ), which point you choose would depend on your research question
I did a simulation with just the molecule I am using for the simulation with the protein. After NPT equilibration I calculated the density of the molecule. When I am plotting the density against time I find that the density is stabilised at around 1010kg/m3 After an initial rise. Now the experimental data says that the density of the molecule is 982kg/m3. Can you please tell me whether this error is acceptable for the simulation or not?
How acceptable that is depends on how fine-grained your study needs to be, the simulations and experiments are unlikely to perfectly match.