I am performing validation study of designed protein (240 AA)through GROMACS. Ideally, pressure should be around 1 barr.However, I have received value of 3.47966 bar during my simulation run. what is the maximum allowed value? How can I justify this value in revision for my article?
over the course of the equilibration, the average value of the pressure is 1.05 bar. It is suggested in Gromacs that, when we change ensemble, add -t command in run input. For example, change from NVT to NPT or form NPT (with Berendsen) to NPT (Noose-Hoover) add -t previous_run. Here are some example commands.
1. Minimization:
gmx grompp -f minimize.mdp -c structure.gro -p topol.top -o min_structure.tpr
gmx mdrun -deffnm min_structure -v -c
2. Then we do NVT
gmx grompp -f nvt.mdp -c min_structure.gro -p topol.top-o nvt.tpr -t min_structure
3. Then we do NPT (Berendsen thermostat)
gmx grompp -f npt-berend.mdp -c nvt.gro -p topol.top -o npt-berend.tpr -t nvt
gmx mdrun -deffnm npt-berend -v -c
4. Then we do NPT (Noose-Hoover)
gmx grompp -f npt-noose-hoover.mdp -c npt-berend.gro -p topol.top -o npt-noose-hoover.tpr -t npt-berend
gmx mdrun -deffnm npt-noose-hoover -v -c
so Rezvan Marjani does that mean adding -t command will help maintaining the pressure?
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