GROMACS version:2025
GROMACS modification: no
Can someone provide me with the tip3p.gro file for this water model and the itp file as well.
Thanks in advance
You can find gro/itp files for different water models where you installed GROMACS, just go into the local directory where_you_installed_gromacs/share/gromacs/top/.
Thanks so much. I found the tip3p.itp file, but not the corresponding gro file. However, I found gro files for other water models. Can I solvate the system using a different water model and still include the tip3p.itp in the topology file?
Hi,
you can use the “spc216.gro” file (default option in gmx solvate) to solvate your system.
Best,
Marius
Thank you so much for your reply. I am using the AMBER ff19SB force field, which is compatible with the OPC or TIP3P water models. My protein is a 767-residue trimer, and when I tried to solvate it using tleap, I encountered many issues. Therefore, I decided to perform the solvation step using GROMACS instead. That why I need the TIP3P specifically.
Yes, you can solvate with gmx solvate, and yes, you can use other water models to solvate. As @Marius said, you can solvate by specifying the flag spc216.gro, even if you will use the TIP3P water model and not the SPC one. The important thing is if it is a three- or a four-point water model as this will influence the structure of the inserted molecules and the total number of atoms. Then the “nature” of the molecule will be decided by the topology that you are using, so if you pass the TIP3P parameters to your topology you will be simulating a TIP3P water model, as long as the number of atoms and their namings are consistent. :)
Thank you so much, sir. I really appreciate your guidance. I will do so. Thanks again for your help.