GROMACS version:2023.5
GROMACS modification: Yes/No
can anybody help me with the dimer preparation with gmx translate to keep two single monomer peptide in a single box within defined distance .
After setting both the monomers in a single box ,after phase 2 Equlibration(NPT) step , when i am visualizing NPT.gro i get to notice the one of monomer peptide is out of the box .
i have tried changing distance between two peptide
my box size 12x12x12 A
That a molecule is (looks like it is) “out of the box” is not a problem, by periodicity it will be inside the box - everything is by definition “inside the box”.
Try visualizing periodic representations in VMD to see if you still think it is a problem.
thank you for your quick reply
i am trying to simulate amyloid beta with Ionic liquid to check whether IL inhibits amyloid aggregation so for this purpose i have used npt ,nvt and md .mdp files from gromacs tutorials is there any changes to be made in .mdp files apart from tc groups and simulation time
If you are using the same force field as in the tutorial, you are probably fine. Otherwise, you’ll need to make sure that, e.g., the electrostatics, van der Waals and constraints settings are suitable for the force field you are using. You might want to have a look at the pressure coupling settings as well, I don’t remember what settings are used in different tutorials. Make sure that you are using c-rescale or make sure that tau-p is OK (high enough) for parrinello-rahman.
You might also want to tweak the output settings.
thank you for your quick reply
i am using #include “amber99sb-ildn.ff/forcefield.itp” this forcefeild with water model tip3p, i have generated topology for ligands from antechamber ( acpype )
is their any specific settings in .mdp files
Have a look at this post: Protein/Ligand complex amber production question - #2 by alevilla and this thread: Mdp parameters for non-bonded interaction using the AMBER force field - #6 by fatemeh. There seems to be a range of “valid” settings for the amber force fields. But the ones in the first post should be OK, as far as I know.