Hi
I used to simulate with 4.6.5 Gromacs but now I have updated it to 2021.6. so there are some orders I don’t know what they are in this new version. for example, I want to simulate a coarse-grained micelle in 4.6.5 Gromacs. I use these orders:
1- genbox -ci P80.gro -nmol 60 -box 11 11 11 -try 500000 -o p.gro -vdwd 0.2 -seed 3
after that, I add frozen water:
2- genbox -cp p.gro -cs BW.gro -o pwf.gro -maxsol 981 -vdwd 0.2
so I try to fill the box with the usual water:
3- 4- genbox -cp pwf.gro -cs water.gro -o pw.gro -maxsol 10000 -vdwd 0.2
for these 3 orders in the new version I use instead of the first order:
1- gmx insert-molecules -ci P80.gro -nmol 60 -box 11 11 11 -o p.gro -try 500000 –seed 3 –radius 0.2
but I don’t know how to add frozen water and usual in continuous. could you please help me?
and also after min, nvt, npt, and md I use these orders for PBC condition and centering in 4.6.5 Gromacs:
4- trjconv -f traj.trr -o micelle_cluster.trr -s topol.tpr -pbc cluster
5- trjconv -f micelle_cluster.trr -o micelle_centered.trr -s topol.tpr –center
would you please help me with what are they in 2021.6 Gromacs?
Best regards,
Shiva
See the document: Command-line reference — GROMACS 2022.3 documentation
genbox has been replaced by gmx solvate.
Tnx a lot