GROMACS version: 2021.3
GROMACS modification: Yes
Hello all,
I am simulating solvation behaviour of carbohydrates in acetic acid and acetone solutions. The parameters for the carbohydrates are taken from GLYCAM06 and force field parameters for acetic acid and acetone were generated by GAFF, through providing charges calculated by Hartree-Fock. All parameters have then be converted to GROMACS format through Acpype, which has been tested by us for quite some years now.
However, I have encountered issues with the NPT step of the simulations, which follows the EM and NVT steps. During this stage, the 505050 nm3 simulation box quickly shrinks to approximately 323232 nm3. The pressure then attempts to reach 1 bar, but remains below that threshold, resulting in slow expansion of the box size and a slow decrease in the overall density. Even after 150 ns of simulation time, the pressure has not yet reached equilibrium.
To adjust the pressure, I am using C-rescale with a relatively high tau of 2-3 ps and a compressibility factor of 10.8e-5 for the solution. However, this has led to a high number of LINCS warnings, which have been followed by domain decomposition errors. These errors stem from the system being inadequately equilibrated, which is precisely what I am attempting to achieve.
Any suggestions?
Kind regards,
Ali