GROMACS version: 2020.3
GROMACS modification: No
I have been attempting to simulate a GFP construct (with a zwitterionic TYG chromophore) in a mixed solvent box with ~8M urea and water in the Amber99 force field, using the TIP3P water model. When I run energy minimization using the steepest descent algorithm, the forces will not converge below 1000 kJ/mol/nm, though the system converges to machine precision. I am hoping someone could advise me on how to fix this such that the forces will converge below 1000 kJ/mol/nm (I am an undergraduate - not an expert).
The specifics of my protocol is as follows:
- I use pdb2gmx to generate a standard topology file, position restraint file and coordinate file
- I use editconf to place the GFP construct in the center of a periodic box such that there is a distance of 1.5 nm between the construct and the box edges
- I use insert-molecules to place 2700 urea molecules in the box
- I solvate with 19000 molecules of TIP3P using the -maxsol option of solvate
- I neutralize the charge of the system with 6 NA ions using genion
Initially, I hypothesized that the forces may be too large as a result of the pressure in the box being too high. As such, I ran short, successive NPT equilibrations (using isotropic Berendsen pressure coupling, PME electrostatics, electrostatic cutoff of 1.2 nm, VDW cutoff of 1.2 nm) to allow the box to expand and contract. This was only successful if I used a time step of 0.4 fs - anything larger produced too many LINCS errors. I ultimately equilibrated the system for 1 ns in total, and was able to reach a desirable potential energy value as well as a desirable average pressure value.
That being said, I remain bothered by the fact that I cannot get the forces to converge below 1000 kJ/mol/nm, and I would like to use a time step that is larger than 0.4 fs if at all possible.
Hence, if anyone has advice for me, I am all ears, and I am eager to learn.
Rensselaer Polytechnic Institute ’22
Undergraduate Researcher, Bystroff Lab
Co-Op Research Assistant, RNA Institute