gmx solvate | -maxsol | Not filling the desired amount of solvent molecules
Summary
This issue refers to the -maxsol
flag in gmx solvate
program.
Exact steps to reproduce
Get the .gro
,.top
and .itp
input files:
]$ git clone https://github.com/DavidCdeB/gmx_solvate.git
]$ cd gmx_solvate
]$ gmx solvate -cp PNP1_GMX.gro -cs spc216.gro -box 3 3 3 -maxsol 886 -o PNP1_GMX_solv.gro -p PNP1_GMX.top
I need to add all 886
water molecules so that I can model the same density.
However, only 879
have been added:
]$ tail -4 PNP1_GMX.top
[ molecules ]
; Compound nmols
PNP1 1
SOL 879
1. Which is the algorithm / criteria used by -maxsol
for not filling the box with the desired amount of water molecules?
A quick look with vmd PNP1_GMX_solv.gro
and pbc box
in console shows there are still what it seems "empty" spaces available in the box.
2. Is there a way to "enforce" those missing 7 water molecules to enter the box?
Many thanks