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 system.top”, I ended up with the following error.
System I/O error: Library file ‘spce216.gro’ not found in current dir nor in the default directories. The following paths were searched:
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).
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.