# Extending the simulation with new mdp file
**URL:** https://gromacs.bioexcel.eu/t/extending-the-simulation-with-new-mdp-file/3460
**Category:** User discussions
**Tags:** mdrun, gmx-trjconv
**Created:** [January 11, 2022, 10:51am UTC](https://gromacs.bioexcel.eu/t/extending-the-simulation-with-new-mdp-file/3460 "2022-01-11T10:51:19Z")
**Posts on this page:** 3
**Page:** 1
### Author:  [@aathithyadiaz](https://gromacs.bioexcel.eu/u/aathithyadiaz)
#### Post date: [January 11, 2022, 10:51am UTC](https://gromacs.bioexcel.eu/t/extending-the-simulation-with-new-mdp-file/3460/1 "2022-01-11T10:51:19Z")
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.
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### Author:  [@hess](https://gromacs.bioexcel.eu/u/hess)
#### Post date: [January 12, 2022, 8:40am UTC](https://gromacs.bioexcel.eu/t/extending-the-simulation-with-new-mdp-file/3460/2 "2022-01-12T08:40:47Z")
The only “error” here is in the precision of the time. In all GROMACS trajectory output, except for the checkpoint file, the time is written in the precision GROMACS was compiled with, which is single precision in your case. In single precision the differences between in time between two steps is smaller than the precision of the floating point number, so you get the same time for adjacent frame. But all other output is correct, so there is no issue if you ignore the time stamp.
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### Author:  [@aathithyadiaz](https://gromacs.bioexcel.eu/u/aathithyadiaz)
#### Post date: [January 20, 2022, 3:52am UTC](https://gromacs.bioexcel.eu/t/extending-the-simulation-with-new-mdp-file/3460/3 "2022-01-20T03:52:04Z")
Thank You! that was helpful. However, in case of the bulk water simulation (200ps), the effect of precision of time/time stamp is not observed.