GROMACS version: 2019
GROMACS modification: No
For extension of the simulation system with different nstxout, I used following gromacs commands
gmx grompp -f new.mdp -c old.tpr -o new.tpr -t old.cpt -p topol.top
gmx mdrun -s new.tpr
My new.mdp file is given below
title = Simulation
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 150001000
dt = 0.002 ; 2 fs
; Output control
nstxout = 2 ; suppress bulky .trr file by specifying
nstvout = 2 ; 0 for output frequency of nstxout,
nstfout = 2 ; nstvout, and nstfout
nstenergy = 2 ; save energies every 10.0 ps
nstlog = 2 ; update log file every 10.0 ps
nstxout-compressed = 2 ; save compressed coordinates every 10.0 ps
compressed-x-grps = System ; save the whole system
; Bond parameters
continuation = yes ; Restarting after NPT
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
; Neighborsearching
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)
; 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 = 300 300 ; reference temperature, one for each group, in K
; 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
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
gen_seed = 2724 ;
However, my output trajectory file shows duplicate time t,
The output trajectory is converted with trjconv into pdb file and the output are as follows
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.00000 step= 150000000
REMARK THIS IS A SIMULATION BOX
CRYST1 93.164 94.633 78.792 90.00 90.00 90.00 P 1 1
MODEL 1
ATOM 1 Na+ Na+ 262 6.840 31.420 15.540 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.000 19.610 9.590 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.420 47.440 43.710 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.360 61.070 4.600 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.00000 step= 150000002
REMARK THIS IS A SIMULATION BOX
CRYST1 93.163 94.632 78.792 90.00 90.00 90.00 P 1 1
MODEL 2
ATOM 1 Na+ Na+ 262 6.850 31.470 15.540 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.000 19.650 9.570 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.390 47.470 43.700 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.370 61.090 4.600 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.00000 step= 150000004
REMARK THIS IS A SIMULATION BOX
CRYST1 93.163 94.632 78.792 90.00 90.00 90.00 P 1 1
MODEL 3
ATOM 1 Na+ Na+ 262 6.880 31.530 15.500 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.030 19.700 9.530 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.370 47.510 43.670 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.400 61.100 4.590 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.00000 step= 150000006
REMARK THIS IS A SIMULATION BOX
CRYST1 93.163 94.632 78.792 90.00 90.00 90.00 P 1 1
MODEL 4
ATOM 1 Na+ Na+ 262 6.920 31.560 15.490 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.060 19.730 9.500 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.370 47.510 43.640 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.440 61.100 4.590 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.03125 step= 150000008
REMARK THIS IS A SIMULATION BOX
CRYST1 93.163 94.632 78.792 90.00 90.00 90.00 P 1 1
MODEL 5
ATOM 1 Na+ Na+ 262 6.940 31.570 15.460 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.080 19.730 9.480 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.340 47.500 43.610 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.450 61.060 4.580 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.03125 step= 150000010
REMARK THIS IS A SIMULATION BOX
CRYST1 93.163 94.632 78.792 90.00 90.00 90.00 P 1 1
MODEL 6
ATOM 1 Na+ Na+ 262 6.940 31.600 15.430 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.070 19.730 9.460 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.310 47.480 43.580 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.460 61.020 4.570 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.03125 step= 150000012
REMARK THIS IS A SIMULATION BOX
CRYST1 93.162 94.631 78.791 90.00 90.00 90.00 P 1 1
MODEL 7
ATOM 1 Na+ Na+ 262 6.920 31.630 15.410 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.050 19.730 9.460 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.270 47.460 43.570 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.440 60.990 4.580 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.03125 step= 150000014
REMARK THIS IS A SIMULATION BOX
CRYST1 93.162 94.631 78.791 90.00 90.00 90.00 P 1 1
MODEL 8
ATOM 1 Na+ Na+ 262 6.960 31.650 15.410 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.100 19.750 9.480 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.280 47.450 43.580 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.480 60.960 4.610 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.03125 step= 150000016
REMARK THIS IS A SIMULATION BOX
CRYST1 93.162 94.631 78.791 90.00 90.00 90.00 P 1 1
MODEL 9
ATOM 1 Na+ Na+ 262 6.990 31.660 15.410 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.130 19.740 9.510 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.310 47.420 43.590 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.530 60.920 4.640 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.03125 step= 150000018
REMARK THIS IS A SIMULATION BOX
CRYST1 93.162 94.631 78.791 90.00 90.00 90.00 P 1 1
MODEL 10
ATOM 1 Na+ Na+ 262 6.990 31.670 15.410 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.140 19.730 9.540 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.300 47.390 43.600 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.540 60.880 4.680 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.03125 step= 150000020
REMARK THIS IS A SIMULATION BOX
CRYST1 93.162 94.631 78.791 90.00 90.00 90.00 P 1 1
MODEL 11
ATOM 1 Na+ Na+ 262 6.960 31.690 15.390 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.120 19.740 9.550 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.290 47.380 43.590 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.530 60.860 4.690 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.03125 step= 150000022
REMARK THIS IS A SIMULATION BOX
CRYST1 93.161 94.630 78.790 90.00 90.00 90.00 P 1 1
MODEL 12
ATOM 1 Na+ Na+ 262 6.930 31.740 15.360 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.120 19.760 9.540 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.280 47.390 43.570 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.520 60.860 4.690 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.06250 step= 150000024
REMARK THIS IS A SIMULATION BOX
CRYST1 93.161 94.630 78.790 90.00 90.00 90.00 P 1 1
MODEL 13
ATOM 1 Na+ Na+ 262 6.950 31.770 15.330 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.150 19.790 9.530 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.320 47.390 43.550 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.560 60.860 4.680 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.06250 step= 150000026
REMARK THIS IS A SIMULATION BOX
CRYST1 93.161 94.630 78.790 90.00 90.00 90.00 P 1 1
MODEL 14
ATOM 1 Na+ Na+ 262 6.990 31.790 15.300 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.230 19.800 9.500 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.400 47.380 43.520 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.630 60.850 4.660 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.06250 step= 150000028
REMARK THIS IS A SIMULATION BOX
CRYST1 93.161 94.630 78.790 90.00 90.00 90.00 P 1 1
MODEL 15
ATOM 1 Na+ Na+ 262 7.030 31.790 15.290 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.290 19.790 9.500 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.480 47.350 43.520 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.690 60.820 4.660 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.06250 step= 150000030
REMARK THIS IS A SIMULATION BOX
CRYST1 93.161 94.630 78.790 90.00 90.00 90.00 P 1 1
MODEL 16
ATOM 1 Na+ Na+ 262 7.020 31.810 15.260 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.310 19.800 9.480 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.520 47.330 43.490 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.710 60.820 4.630 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.06250 step= 150000032
REMARK THIS IS A SIMULATION BOX
CRYST1 93.161 94.630 78.790 90.00 90.00 90.00 P 1 1
MODEL 17
ATOM 1 Na+ Na+ 262 7.000 31.840 15.240 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.300 19.810 9.450 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.540 47.320 43.470 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.700 60.830 4.600 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.06250 step= 150000034
REMARK THIS IS A SIMULATION BOX
CRYST1 93.161 94.630 78.790 90.00 90.00 90.00 P 1 1
MODEL 18
ATOM 1 Na+ Na+ 262 6.950 31.880 15.240 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.280 19.840 9.440 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.540 47.330 43.470 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.660 60.850 4.580 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.06250 step= 150000036
REMARK THIS IS A SIMULATION BOX
CRYST1 93.161 94.630 78.790 90.00 90.00 90.00 P 1 1
MODEL 19
ATOM 1 Na+ Na+ 262 6.920 31.940 15.230 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.270 19.860 9.420 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.550 47.340 43.470 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.640 60.870 4.560 1.00 0.00 Na
TER
ENDMDL
REMARK GENERATED BY TRJCONV
TITLE Generic title t= 300000.06250 step= 150000038
REMARK THIS IS A SIMULATION BOX
CRYST1 93.161 94.630 78.790 90.00 90.00 90.00 P 1 1
MODEL 20
ATOM 1 Na+ Na+ 262 6.890 31.960 15.210 1.00 0.00 Na
ATOM 2 Na+ Na+ 263 26.270 19.860 9.410 1.00 0.00 Na
ATOM 3 Na+ Na+ 264 17.560 47.300 43.460 1.00 0.00 Na
ATOM 4 Na+ Na+ 265 91.620 60.850 4.540 1.00 0.00 Na
TER
ENDMDL
Can someone help in pointing out the error in the steps used for simulation extension?
Thank You.