# Need to create water simulation box using spce water model **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx, forcefield, mdrun, simulation-setup\ **Created:** [July 18, 2022, 2:54am UTC](https://gromacs.bioexcel.eu/t/need-to-create-water-simulation-box-using-spce-water-model/4477 "2022-07-18T02:54:04Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![Kal](https://avatars.discourse-cdn.com/v4/letter/k/9de053/32.png) [@Kal](https://gromacs.bioexcel.eu/u/Kal)\ **Post date:** [July 18, 2022, 2:54am UTC](https://gromacs.bioexcel.eu/t/need-to-create-water-simulation-box-using-spce-water-model/4477/1 "2022-07-18T02:54:04Z")
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:_ - /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 https://www.gromacs.org documentation](http://www.gromacs.org/Documentation/Errors)_ I need to resolve this problem. ---
**Author:** ![pjohansson](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pjohansson/32/316_2.png) [@pjohansson](https://gromacs.bioexcel.eu/u/pjohansson)\ **Post date:** [July 18, 2022, 6:48am UTC](https://gromacs.bioexcel.eu/t/need-to-create-water-simulation-box-using-spce-water-model/4477/2 "2022-07-18T06:48:46Z")
Hi, 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](https://manual.gromacs.org/2021-current/install-guide/index.html#getting-access-to-gromacs-after-installation) ---
**Author:** ![ostueker](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ostueker/32/4918_2.png) [@ostueker](https://gromacs.bioexcel.eu/u/ostueker)\ **Post date:** [July 20, 2022, 1:33am UTC](https://gromacs.bioexcel.eu/t/need-to-create-water-simulation-box-using-spce-water-model/4477/3 "2022-07-20T01:33:55Z")
> [@Kal](#): > > “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._ 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: ```auto gmx solvate -cs spc216.gro -o water.pdb -box 2.5 2.5 2.5 -p system.Top ``` Happy simulating, Oliver ---
**Author:** ![Kal](https://avatars.discourse-cdn.com/v4/letter/k/9de053/32.png) [@Kal](https://gromacs.bioexcel.eu/u/Kal)\ **Post date:** [July 20, 2022, 6:31am UTC](https://gromacs.bioexcel.eu/t/need-to-create-water-simulation-box-using-spce-water-model/4477/4 "2022-07-20T06:31:23Z")
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. Cheers, Kal ---
**Author:** ![ostueker](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/ostueker/32/4918_2.png) [@ostueker](https://gromacs.bioexcel.eu/u/ostueker)\ **Post date:** [July 20, 2022, 11:42am UTC](https://gromacs.bioexcel.eu/t/need-to-create-water-simulation-box-using-spce-water-model/4477/5 "2022-07-20T11:42:53Z")
After running: ```auto 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. ---
**Author:** ![Kal](https://avatars.discourse-cdn.com/v4/letter/k/9de053/32.png) [@Kal](https://gromacs.bioexcel.eu/u/Kal)\ **Post date:** [July 23, 2022, 1:48pm UTC](https://gromacs.bioexcel.eu/t/need-to-create-water-simulation-box-using-spce-water-model/4477/6 "2022-07-23T13:48:28Z")
Thank you ---
**Author:** ![Kal](https://avatars.discourse-cdn.com/v4/letter/k/9de053/32.png) [@Kal](https://gromacs.bioexcel.eu/u/Kal)\ **Post date:** [July 23, 2022, 1:49pm UTC](https://gromacs.bioexcel.eu/t/need-to-create-water-simulation-box-using-spce-water-model/4477/7 "2022-07-23T13:49:40Z")
Thank you!