GROMACS version:2019
GROMACS modification: No
Hi
I want to simulation of carbon dioxide (Co2) with gromacs in gas phase state, but after NPT run, I get wrong mass density near 1100kg/m3 (real density 1.7 kg/m3) why?
I used values for compressibility default, 4.5e-5.
I calculated mass density with gmx energy.
force field: opls and amber (check two forms)
thanks
As I sent to you in your ResearchGate message:
Using liquid water compressibility with a barostat will force your system into an unphysical liquid state. Simulations of gases should be done using an NVT ensemble. Please ask all future GROMACS questions via the GROMACS users forum.
Is it not possible to run NPT gmx in the gas phase? I want to calculate the density of the gas at a given pressure. I then want to calculate the self-solvation free energy (residual chemical potential) of the gas using the resulting box size.
If you attempt to apply a barostat to a gas-phase system, it will quickly collapse into a liquid because the barostat will compress the box. You could use NVT to have a fixed box size, but that’s the only real solution.
Has anyone tried a Monte Carlo barostat in conjunction with a gmx thermostat for a gas phase?
Monte Carlo simulation packages work fine for a gas phase, and their pressure change is essentially based on a “test squeezing of the box”.
Given that there is no MC barostat in GROMACS, I doubt it.
What if the gas doesn’t liquefy when it should? I am running NPT simulations of light hydrocarbons with OPLS and get a good match on gas densities but lowering the temperature below the evaparation point does not lead to the appearance of liquid phase