# How to get potential energy of a single water molecule with the rest of the system **URL:** \ **Category:** User discussions\ **Created:** [January 27, 2021, 12:31am UTC](https://gromacs.bioexcel.eu/t/how-to-get-potential-energy-of-a-single-water-molecule-with-the-rest-of-the-system/1492 "2021-01-27T00:31:06Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![PanyueW](https://avatars.discourse-cdn.com/v4/letter/p/ecc23a/32.png) [@PanyueW](https://gromacs.bioexcel.eu/u/PanyueW)\ **Post date:** [January 27, 2021, 12:31am UTC](https://gromacs.bioexcel.eu/t/how-to-get-potential-energy-of-a-single-water-molecule-with-the-rest-of-the-system/1492/1 "2021-01-27T00:31:06Z")
GROMACS version: 2020 GROMACS modification: No I am trying to get the interaction energy of one water molecule with the rest of the system over an MD trajectory. First I defined a group in the index file call “BULK\_H2O,” then I added this group to the mdp energy group option. I ran the MD for 10 ps and got the edr file. Finally, I use gmx energy to get the potential energy of this water molecule, but I am getting zeros for all kinds of interactions (LJ and coulomb). The defines are there for position restraints of protein and ligand respectively. Here’s my mdp: define = -DPOSRES -DPOSRES\_LIGAND -DPOSRES\_FC\_HG=1000 -DPOSRES\_FC\_HG\_C=1000 -DPOSRES\_FC=1000 integrator = sd dt = 0.001 tinit = 0 nsteps = 10000 ; 10 ps nstxout = 0 ; every 0.5 ps nstvout = 0 nstfout = 0 nstxtcout = 500 ; every 0.5 ps nstenergy = 500 energygrps = BULK\_H2O BULK\_rest comm\_mode = None constraint\_algorithm = lincs lincs\_iter = 2 constraints = all-bonds nstlist = 20 ns\_type = grid rlist = 1.4 rcoulomb = 1.2 rvdw = 1.2 Tcoupl = no; tc\_grps = System tau\_t = 2 ref\_t = 310 Pcoupl = no pcoupltype = isotropic tau\_p = 1.0 compressibility = 4.5e-5 ref\_p = 1.0 refcoord\_scaling = com pbc = xyz gen\_vel = yes gen\_temp = 310 gen\_seed = 290389 ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 27, 2021, 2:00pm UTC](https://gromacs.bioexcel.eu/t/how-to-get-potential-energy-of-a-single-water-molecule-with-the-rest-of-the-system/1492/2 "2021-01-27T14:00:31Z")
> [@PanyueW](#): > > Finally, I use gmx energy to get the potential energy of this water molecule, but I am getting zeros for all kinds of interactions (LJ and coulomb). I’m guessing you ran your simulation on a GPU, which cannot handle different energy groups. In any case, this is an analysis method and shouldn’t really be invoked during the run, anyway. Use `mdrun -rerun` on CPU only to recalculate the interaction energies. ---
**Author:** ![PanyueW](https://avatars.discourse-cdn.com/v4/letter/p/ecc23a/32.png) [@PanyueW](https://gromacs.bioexcel.eu/u/PanyueW)\ **Post date:** [January 29, 2021, 5:02pm UTC](https://gromacs.bioexcel.eu/t/how-to-get-potential-energy-of-a-single-water-molecule-with-the-rest-of-the-system/1492/4 "2021-01-29T17:02:26Z")
Hi, thanks for the reply. Indeed I have run my MD on a GPU. I have tried “gmx mdrun -rerun md.xtc -nb cpu,” but I am still getting 0 for the interaction energies. I do have values for total potential though. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 29, 2021, 5:35pm UTC](https://gromacs.bioexcel.eu/t/how-to-get-potential-energy-of-a-single-water-molecule-with-the-rest-of-the-system/1492/5 "2021-01-29T17:35:52Z")
Which energy terms are you analyzing? ---
**Author:** ![PanyueW](https://avatars.discourse-cdn.com/v4/letter/p/ecc23a/32.png) [@PanyueW](https://gromacs.bioexcel.eu/u/PanyueW)\ **Post date:** [January 29, 2021, 5:52pm UTC](https://gromacs.bioexcel.eu/t/how-to-get-potential-energy-of-a-single-water-molecule-with-the-rest-of-the-system/1492/7 "2021-01-29T17:52:10Z")
LJ-SR and Coulomb-SR of my water molecule vs. the rest of the system. ---
**Author:** ![gvigers](https://avatars.discourse-cdn.com/v4/letter/g/a9a28c/32.png) [@gvigers](https://gromacs.bioexcel.eu/u/gvigers)\ **Post date:** [April 1, 2022, 6:41pm UTC](https://gromacs.bioexcel.eu/t/how-to-get-potential-energy-of-a-single-water-molecule-with-the-rest-of-the-system/1492/8 "2022-04-01T18:41:41Z")
I’m seeing the same thing. This is the third thread that I’ve found with a very similar problem but without a resolution. Is there anyone that I can work with on this? I’m happy to upload files or work with a developer directly. Just let me know! Thank you Guy Vigers