Need to create water simulation box using spce water model

GROMACS version: 2021.2
GROMACS modification: No
Here post your question -
I need to create a water simulation box with the SPCE water model.
when I gave the following command
“gmx solvate -cs spce216.gro -o water.pdb -box 2.5 2.5 2.5 -p”, I ended up with the following error.

System I/O error:
Library file ‘spce216.gro’ not found in current dir nor in the default
The following paths were searched:

  • /home/jc818833/jc818833/research/Chlorine/water-cl02 (current dir)*
  • /usr/share/gromacs/top (default)*
    You can set additional directories to search with the GMXLIB path variable.

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage documentation

I need to resolve this problem.


What directory is Gromacs installed into? Are you sourcing* the GMXRC file from [that dir]/bin, or does that fix your problem?

If you installed through a package manager and you can’t find GMXRC, try setting+exporting the GMXLIB variable to the top directory in the installation directory (often found at [installation dir]/share/gromacs/top).

* See: Getting access to GROMACS after installation

Both SPC and SPC/E are three-point water models that just differ in the parameters applied. Therefore having more than a single box with water molecules would be redundant.

Just use:

gmx solvate -cs spc216.gro -o water.pdb -box 2.5 2.5 2.5 -p system.Top

Happy simulating,

Hi Oliver,

Thank you very much for your reply.

The literature review I am referring to do these simulations used the SPC/E water model.
I cannot compare my simulation results with those papers since I cannot use this SPC/E model.


After running:

gmx solvate -cs spc216.gro -o water.pdb -box 2.5 2.5 2.5 -p system.Top

all you have is a coordinate file with box definitions that is filled with triples of coordinates (conveniently called OW, HW1 and HW2) and that are arranged in a way that the HW1-OW-HW2 angle is \approx 109.47°.

This is neither SPC, SPC/E nor TIP3P at this point, because you haven’t yet applied any topology.

You can use the same coordinate file to simulate SPC, SPC/E ot TIP3P water by including the right water parameters (spce.itp , spc.itp or tip3p.itp) when generating your TPR file with grompp.

If you were to simulate a 4-point or 5-point water model, you would need to use a different coordinate file, that has the correct number of correctly named “dummy atoms” at the right locations.

Thank you

Thank you!