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.
$ 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
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