I suspect you've just made a typo somewhere in your command; a box-solute distance of 0.1 nm would result in almost no waters being added; there's no way that over a million atoms are going to be output. Be careful that you didn't accidentally specify -d 10 (e.g. Angstom instead of nm) as people often do.

I checked and I think I'm doing it ok according to the tutorial . Follow bellow the steps. (I'm using 2018 version). It was indicated a warning about " Masses and atomic (Van der Waals) radii", could be the problem?

gmx_mpi editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 0.5

Note that major changes are planned in future for editconf, to improve usability and utility.Read 1932 atoms

Volume: 64.3909 nm^3, corresponds to roughly 28900 electrons

No velocities found

system size : 21.051 10.285 15.882 (nm)

diameter : 26.887 (nm)

center :-18.753 8.441-12.268 (nm)

box vectors : 3.791 3.554 4.779 (nm)

box angles : 90.00 90.00 90.00 (degrees)

box volume : 64.39 (nm^3)

shift : 39.668 12.474 22.127 (nm)

new center : 20.915 20.915 9.859 (nm)

new box vectors : 27.887 27.887 27.887 (nm)

new box angles : 60.00 60.00 90.00 (degrees)

new box volume :15334.80 (nm^3)

GROMACS reminds you: "The last good thing written in C was Franz Schubert's Symphony Number 9." (Erwin Dieterich)

gmx_mpi solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro

WARNING: Masses and atomic (Van der Waals) radii will be guessed

based on residue and atom names, since they could not be

definitively assigned from the information in your input

files. These guessed numbers might deviate from the mass

and radius of the atom type. Please check the output

files if necessary.

NOTE: From version 5.0 gmx solvate uses the Van der Waals radii

from the source below. This means the results may be different

compared to previous GROMACS versions.

Generating solvent configuration

Will generate new solvent configuration of 15x15x11 boxes

Solvent box contains 1566000 atoms in 522000 residues

Removed 61494 solvent atoms due to solvent-solvent overlap

Removed 1761 solvent atoms due to solute-solvent overlap

Sorting configuration

Found 1 molecule type:

SOL ( 3 atoms): 500915 residues

Generated solvent containing 1502745 atoms in 500915 residues

Writing generated configuration to solv.gro

Output configuration contains 1504677 atoms in 501032 residues

Volume : 15334.8 (nm^3)

Density : 978.779 (g/l)

Number of solvent molecules: 500915

Processing topology

Adding line for 500915 solvent molecules with resname (SOL) to topology file (topol.top)

Justin Lemkul thanks in advance! :)

The note about masses is irrelevant and happens whenever any tool reads a coordinate file without a topology (which you don't need to do here).

Your system is "small" in terms of the number of atoms but it is not actually small:

system size : 21.051 10.285 15.882 (nm)

I'm guessing those atoms are in a fully extended configuration.

Using a buffer of 0.5 nm is inadequate to prevent artifacts from the required cutoffs. You should not try shortcuts just to have fewer atoms; you will potentially have a simulation full of artifacts. To do your simulation properly will simply be very expensive.

What do you mean with " fully extended configuration"? How can I check this? Is that a problem to do the MD, if yes, is possible to solve? (My pdb files are from Molegro virtual docker, could be related to this?).

thanks Justin Lemkul !

Check it with visualization. You have few atoms but they extend over a large space, as shown by editconf. I have no experience with Molegro so I can't advise you there. But the physical dimensions of your solute are huge, so you should expect the resulting box to be, as well.

Hi Caroline Frietas,

Please check visualization using chimera or .gro viewer.

Justin Lemkul and Muthusaravanan Sivaramakrishnan I tried to visualize using VMD and chimera, but both were unable to open the solv.gro or newbox.gro files.

That means the file format is wrong, which is likely why you're getting strange box dimensions. My guess is that Molegro has given you an incorrect file to start with. The file format is fixed, and is described in the manual.

Try any other software: autodock, Schrodinger for the preparation and use online server: .gro viewer. Also try different box type cubic, etc.