# What do I do when I don't see density in my gromacs energy selection **URL:** \ **Category:** User discussions\ **Tags:** analysis-tools\ **Created:** [February 8, 2024, 5:08am UTC](https://gromacs.bioexcel.eu/t/what-do-i-do-when-i-dont-see-density-in-my-gromacs-energy-selection/8282 "2024-02-08T05:08:07Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![dlwlrma](https://avatars.discourse-cdn.com/v4/letter/d/3bc359/32.png) [@dlwlrma](https://gromacs.bioexcel.eu/u/dlwlrma)\ **Post date:** [February 8, 2024, 5:08am UTC](https://gromacs.bioexcel.eu/t/what-do-i-do-when-i-dont-see-density-in-my-gromacs-energy-selection/8282/1 "2024-02-08T05:08:08Z")
GROMACS version: 2023.2 GROMACS modification: No I tried to proceed with NPT as usual in protein MD simulation in water and get the density for the whole system. However, I don’t see any “density” items in my “gmx energy” selection. The same symptoms appear when I transfer a project file to my desktop because I suspect an abnormality in the installed equipment. I can be sure that I did not confuse NVT result file with NPT result file. How can I solve this problem? I attach the output of the terminal and the contents of the mdp file used for the NPT. ```auto --- gmx energy -f npt.edr -o density-after-npt.xvg :-) GROMACS - gmx energy, 2023.2 (-: Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Working dir: /home/user1/gmx-workdata/TEAD-YAP-80mM Command line: gmx energy -f npt.edr -o density-after-npt.xvg Opened npt.edr as single precision energy file Select the terms you want from the following list by selecting either (part of) the name or the number or a combination. End your selection with an empty line or a zero. ------------------------------------------------------------------- 1 Bond 2 U-B 3 Proper-Dih. 4 Improper-Dih. 5 CMAP-Dih. 6 LJ-14 7 Coulomb-14 8 LJ-(SR) 9 Disper.-corr. 10 Coulomb-(SR) 11 Coul.-recip. 12 Position-Rest. 13 Potential 14 Kinetic-En. 15 Total-Energy 16 Conserved-En. 17 Temperature 18 Pres.-DC 19 Pressure 20 Constr.-rmsd 21 Vir-XX 22 Vir-XY 23 Vir-XZ 24 Vir-YX 25 Vir-YY 26 Vir-YZ 27 Vir-ZX 28 Vir-ZY 29 Vir-ZZ 30 Pres-XX 31 Pres-XY 32 Pres-XZ 33 Pres-YX 34 Pres-YY 35 Pres-YZ 36 Pres-ZX 37 Pres-ZY 38 Pres-ZZ 39 #Surf*SurfTen 40 T-Protein 41 T-non-Protein 42 Lamb-Protein 43 Lamb-non-Protein ``` ```auto title = OPLS Lysozyme NPT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 2500000 ; 2 * 2500000 = 5000 ps = 5 ns dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps ; Bond parameters continuation = yes ; Restarting after NVT constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Nonbonded settings cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) DispCorr = EnerPres ; account for cut-off vdW scheme ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 310.15 310.15 ; reference temperature, one for each group, in K = 310.15k = 37C ; Pressure coupling is on pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype = isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar = 1bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 refcoord_scaling = com ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Velocity generation gen_vel = no ; Velocity generation is off ``` ---
**Author:** ![throughalfanoir](https://avatars.discourse-cdn.com/v4/letter/t/d78d45/32.png) [@throughalfanoir](https://gromacs.bioexcel.eu/u/throughalfanoir)\ **Post date:** [February 8, 2024, 11:55am UTC](https://gromacs.bioexcel.eu/t/what-do-i-do-when-i-dont-see-density-in-my-gromacs-energy-selection/8282/2 "2024-02-08T11:55:21Z")
What happens if you try to run gmx density on your system? ---
**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\ **Post date:** [February 8, 2024, 12:03pm UTC](https://gromacs.bioexcel.eu/t/what-do-i-do-when-i-dont-see-density-in-my-gromacs-energy-selection/8282/3 "2024-02-08T12:03:40Z")
You must have mixed up your energy file with one from a non-NPT simultion. With NPT you always get the volume and density and without pressure coupling you don’t.