Creating a water sphere around small molecule

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Hi,
I am new to gromacs and I am trying to solvate small organic molecule (dimethylaniline) with water .But I am having a problem with creating a sphere in gromacs,I do have a script that I used for NAMD where I first created water box then upload the pdb file in VMD and use the script to carve it into a sphere.
So, I would like to know is there any direct way in gromacs that I can create a water sphere around the molecule.

So far I have minimized and equilibrated dimethylaniline molecule in very large box (999.9nm) as I want to imply no PBC (pseudo-pbc) ,

  1. gmx editconf -f dma_pdb -dma.grp -box 999.9 999.9 999.9
  2. gmx grompp -f min.mdp -c dma.gro -p dma.top -o dma_em.tpr
  3. gmx mdrun -v -deffnm dma_em

Any insights about this is highly appreciate
Thank you

2

And use the -shell option is likely to do what you want.

There are also scripts around that you can put molecules into particular arrangements, web search will pull them up.