# Calculation of Total Energy of the protein **URL:** \ **Category:** User discussions\ **Created:** [May 26, 2022, 12:49pm UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219 "2022-05-26T12:49:51Z")\ **Posts on this page:** 16\ **Page:** 1
**Author:** ![D429321](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@D429321](https://gromacs.bioexcel.eu/u/D429321)\ **Post date:** [May 26, 2022, 12:49pm UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/1 "2022-05-26T12:49:51Z")
GROMACS version: 5.1.5 GROMACS modification: No Respected community members, I am a beginner in Gromacs. I have performed a 50 ns protein in water simulation. Now I would like to calculate the Total energy of my protein with respect to the time. I have followed what was mentioned in the Analysis part of the Protein-Ligand Tutorials. First, I downloaded the mdp file that was linked to that page. I editted two main things in that file. Firstly, I changed energygrps = Protein, and secondly I changed the tc-grps = Protein Non-Protein (Since in that mdp file it was Protein\_JZ4 Water\_and\_ions). I saved my editted mdp file as e.mdp. Then I used the grompp to convert e.mdp into e.tpr file using the following command: gmx grompp -f e.mdp -c npt.gro -t npt.cpt -p topol.top -o e.tpr Next, I used mdrun with the -rerun option to recalculate the energy from the existing simulation trajectory by executing the following command: gmx mdrun -deffnm e -rerun md.xtc -nb cpu After executing the command I got the following warning message: WARNING: Some frames do not contain velocities. Ekin, temperature and pressure are incorrect, the virial will be incorrect when constraints are present. After this an e.edr file was successfully generated and then I used the following command gmx energy -f ie.edr -o energy.xvg After this I selected the Total Energy (13) option from the interactive menu and got the Total Energy Graph. However, I feel due to the above Warning message my result is not accurate (since the velocities are missing). What can I do now to avoid the above warning and get the accurate result. Please guide me. Thanks in advance. ---
**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:** [May 26, 2022, 1:05pm UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/2 "2022-05-26T13:05:56Z")
> [@D429321](#): > > I changed energygrps = Protein This does not cause only the protein’s energy to be written. `energygrps` are only for decomposition of short-range nonbonded energies. > [@D429321](#): > > I feel due to the above Warning message my result is not accurate (since the velocities are missing). In this case, the total energy reported is the same as the potential energy of the system, since there is no kinetic energy. There are a couple of points to make here. The “total energy of the protein” is a physically meaningless quantity. If you want to calculate it, the only way to do so is to strip only the protein coordinates out of the trajectory and make a matching `.tpr` file with `convert-tpr` and use `mdrun -rerun`. But again I emphasize, this quantity means nothing. Force fields are not parametrized to reproduce absolute potential energies of configurations, and kinetic energy is a function of the temperature of the system. ---
**Author:** ![D429321](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@D429321](https://gromacs.bioexcel.eu/u/D429321)\ **Post date:** [May 26, 2022, 1:25pm UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/3 "2022-05-26T13:25:12Z")
Thanks Dr. Lemkul for replying to my question. Sir can you please share the command by which I can strip the protein coordinates alone and make a new .tpr file. Many thanks for you help sir. ---
**Author:** ![D429321](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@D429321](https://gromacs.bioexcel.eu/u/D429321)\ **Post date:** [May 27, 2022, 9:46am UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/4 "2022-05-27T09:46:48Z")
Dr. Lemkul as you mentioned, I have converted my md.tpr file by using the following command: gmx convert-tpr -s md\_0\_50.tpr -o protein.tpr In the interactive menu I selected option 1 for Protein. Then i used the command: gmx mdrun -deffnm protein -rerun md\_0\_50.xtc -nb cpu Upon running this command I encountered the following error: Fatal error: Number of atoms in trajectory (49891) does not match the run input file (3363). Now I understand that the number of atoms in my md\_0\_50.xtc file do not match the number of molecules in the protein.tpr file since the latter file contains only protein. Thus, I tried to extract only the protein trajectory from md\_0\_50.xtc file by using the command: gmx trjconv -f md\_0\_50.xtc -s md\_0\_50.tpr -o protein.xtc Then, from the interactive menu I selected option 1 for protein and got the protein.xtc file. One question that I would like to ask here is my selection for -s in the above command is md\_0\_50.tpr. Is this correct? At this point I would also like to mention that my original md\_0\_50.xtc was generated but using md.mdp that did not specify any energygrps. Is this OK? Then again I executed the command gmx mdrun -deffnm protein -rerun protein.xtc -nb cpu This time there was successful execution but I got the same WARNING again stating WARNING: Some frames do not contain velocities. ``` Ekin, temperature and pressure are incorrect, the virial will be incorrect when constraints are present. ``` Dr. Lemkul I suspect after doing all this the velocities are still missing. Now how can I proceed from here onwards? Kindly give your valuable suggestion. Thanks in advance. ---
**Author:** ![D429321](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@D429321](https://gromacs.bioexcel.eu/u/D429321)\ **Post date:** [May 28, 2022, 2:11pm UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/5 "2022-05-28T14:11:02Z")
A new update… I figured out that my working directory does not have an md\_0\_50.trr file that’s why the velocities are missing. Actually this file was never generated in my original simulation. So what I have done is I have run my simulation again from scratch with an updated md.mdp file with the following changes so that the md\_0\_50.trr file gets generated. nstxout = 5000 ; save coordinates every 10.0 ps nstvout = 5000 ; save velocities every 10.0 ps Now, after the simulation got over I have used the following command to generate a new .xtc file from my .trr file. I have used the following command to do this: gmx trjconv -s md\_0\_50.tpr -f md\_0\_50.trr -o protein.xtc In the interactive menu I selected option 1 for Protein. Now my xtc file contains only protein coordinates and velocities. Since I will use -rerun so I generated a new .tpr file that contains the protein coordinates alone. I generated this .trp file by using the command gmx convert-tpr -s md\_0\_50.tpr -o protein.tpr. From the interactive menu I selected the option 1 for protein. So now I have both the protein.xtc file (containing coordinates and velocity data of proteins) and protein.tpr file. Next I executed -rerun by applying the command: gmx mdrun -deffnm protein protein.xtc -nb cpu The resulting command gave me the output file protein.edr Then by using the command gmx energy -f protein.edr -o Total\_energy.xvg I got the value and graph. Since I am a beginner in gromacs I would be extremely grateful to any expert in Gromacs who can go through my procedure and confirm that whatever I have done is correct. Please help me. Thanks in advance. ---
**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:** [May 31, 2022, 2:43am UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/6 "2022-05-31T02:43:14Z")
The procedure is correct, but again I caution that the value you obtain has no physical meaning. ---
**Author:** ![D429321](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@D429321](https://gromacs.bioexcel.eu/u/D429321)\ **Post date:** [May 31, 2022, 10:03am UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/7 "2022-05-31T10:03:00Z")
Many thanks Dr. lemkul for your confirmation. I am aware that this quantity may not be that much significant. I was just interested in finding this out as I was comparing my results with the previously published data. Once again thanks for your kind support. ---
**Author:** ![D429321](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@D429321](https://gromacs.bioexcel.eu/u/D429321)\ **Post date:** [June 6, 2022, 12:45pm UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/8 "2022-06-06T12:45:31Z")
There is another update in this post. Recently i have run another protein in water simulation for 100 ns. My md.mdp file had nstxout = 5000 ; save coordinates every 10.0 ps nstvout = 5000 ; save velocities every 10.0 ps So that the .trr file gets generated. And then inorder to calculate the total energy i made a new tpr file containing only protein coordinates (convert-tpr -s md\_0\_100.tpr -o protein.tpr. Then i also made another xtc file from the trr file (gmx trjconv -s md\_0\_100.tpr -f md\_0\_100.trr -o protein.xtc. (selected protein when prompted). Then when i gave the command gmx mdrun -deffnm protein -rerun protein.xtc -nb cpu, i got the same warning as follows \\ WARNING: Some frames do not contain velocities Ekin, temperature and pressure are incorrect, the virial will be incorrect I am not able to understand why is this happening? I have .trr file also which has the velocities then why it says “some frames do not contain velocities”. Please give your valuable suggestion. Thanks in advance ---
**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:** [June 6, 2022, 1:15pm UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/9 "2022-06-06T13:15:20Z")
The `.trr` file is the only one with velocities. An `.xtc` file only ever has coordinates. ---
**Author:** ![D429321](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@D429321](https://gromacs.bioexcel.eu/u/D429321)\ **Post date:** [June 6, 2022, 1:40pm UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/10 "2022-06-06T13:40:08Z")
Then in that case how can i avoid this error? Please suggest some solution sir. ---
**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:** [June 6, 2022, 2:08pm UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/11 "2022-06-06T14:08:39Z")
If you need velocities, use the file that contains them (the `.trr` file). Conversion to `.xtc` format makes no sense if you need velocities, because you lose them there. ---
**Author:** ![D429321](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@D429321](https://gromacs.bioexcel.eu/u/D429321)\ **Post date:** [June 7, 2022, 4:19am UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/12 "2022-06-07T04:19:39Z")
Sir thank you for your response. I already have the protein.tpr file that contains the protein coordinates. Then i used the command gmx trjconv -s md\_0\_100.tpr -f md\_0\_100.trr -o protein.trr and selected (protein) #1 when prompted. As a result of this i have the protein.trr file. Now, when I executed the command gmx mdrun -deffnm protein -rerun protein.trr -nb cpu I got the following error: Back Off! I just backed up protein.trr to ./#protein.trr.1# starting md rerun ‘Protein in water’, reading coordinates from input trajectory ‘protein.trr’ Last frame -1 time 0.000 * * * Program gmx mdrun, VERSION 5.1.4 Source code file: /home/guest/gromacs/gromacs-5.1.4/src/programs/mdrun/md.cpp, line: 685 Fatal error: Number of atoms in trajectory (-1) does not match the run input file (3372). Please give some suggestion. Thanks in advance. ---
**Author:** ![D429321](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@D429321](https://gromacs.bioexcel.eu/u/D429321)\ **Post date:** [June 7, 2022, 11:18am UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/13 "2022-06-07T11:18:22Z")
Dr. Lemkul please give your valuable suggestion so that I can overcome this problem. ---
**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:** [June 8, 2022, 2:14am UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/14 "2022-06-08T02:14:45Z")
No idea. What does `gmx check` tell you about the `md_0_100.trr` and `protein.trr` files? ---
**Author:** ![D429321](https://avatars.discourse-cdn.com/v4/letter/d/958977/32.png) [@D429321](https://gromacs.bioexcel.eu/u/D429321)\ **Post date:** [June 8, 2022, 6:19am UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/15 "2022-06-08T06:19:52Z")
Dr. Lemkul I used the command: gmx check -f md\_0\_100.trr -f2 protein.trr. Lot of output was printed on the terminal and I am pasting the output printed in the beginning and at the very end: gmx check -f md\_0\_100.trr -f2 protein.trr Comparing trajectory files md\_0\_100.trr and protein.trr trn version: GMX\_trn\_file (single precision) Reading frame 0 time 0.000 natoms (49891 - 3363) Reading frame 1 time 10.000 natoms (49891 - 3363) Reading frame 2 time 20.000 natoms (49891 - 3363) Reading frame 3 time 30.000 natoms (49891 - 3363) Reading frame 4 time 40.000 natoms (49891 - 3363) Reading frame 5 time 50.000 natoms (49891 - 3363) Reading frame 6 time 60.000 natoms (49891 - 3363) Reading frame 7 time 70.000 natoms (49891 - 3363) Reading frame 8 time 80.000 natoms (49891 - 3363) Reading frame 9 time 90.000 natoms (49891 - 3363) Reading frame 10 time 100.000 natoms (49891 - 3363) Reading frame 11 time 110.000 natoms (49891 - 3363) Reading frame 12 time 120.000 natoms (49891 - 3363) Reading frame 13 time 130.000 natoms (49891 - 3363) Reading frame 14 time 140.000 natoms (49891 - 3363) Reading frame 15 time 150.000 natoms (49891 - 3363) Reading frame 16 time 160.000 natoms (49891 - 3363) Reading frame 17 time 170.000 natoms (49891 - 3363) Reading frame 18 time 180.000 natoms (49891 - 3363) Reading frame 19 time 190.000 natoms (49891 - 3363) Reading frame 20 time 200.000 natoms (49891 - 3363) natoms (49891 - 3363) Reading frame 10000 time 100000.000 natoms (49891 - 3363) Last frame 10000 time 100000.000 Last frame 10000 time 100000.000 Both files read correctly. The protein.trr file is obviously smaller as it only contains information related to protein since I generated this by using the command gmx trjconv -s md\_0\_100.tpr -f md\_0\_100.trr -o protein.trr and selected (protein) #1. Kindly look into this and give your valuable suggestions sir. Many thanks for your support. ---
**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:** [June 10, 2022, 4:12am UTC](https://gromacs.bioexcel.eu/t/calculation-of-total-energy-of-the-protein/4219/16 "2022-06-10T04:12:32Z")
If `gmx check` reports normal contents of `protein.trr` then there is some problem in `mdrun` but you should not be trying to do this kind of calculation with a wildly outdated version of the software (5.1.4) that isn’t even supported any more. If you can reproduce the issue with the latest version, file a bug report.