# Is it possible to continue simulation without .cpt file when I have .trr and .xtc file **URL:** \ **Category:** User discussions\ **Created:** [March 22, 2021, 2:22pm UTC](https://gromacs.bioexcel.eu/t/is-it-possible-to-continue-simulation-without-cpt-file-when-i-have-trr-and-xtc-file/1796 "2021-03-22T14:22:35Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![JakubH](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@JakubH](https://gromacs.bioexcel.eu/u/JakubH)\ **Post date:** [March 22, 2021, 2:22pm UTC](https://gromacs.bioexcel.eu/t/is-it-possible-to-continue-simulation-without-cpt-file-when-i-have-trr-and-xtc-file/1796/1 "2021-03-22T14:22:35Z")
GROMACS version:2020\_2 GROMACS modification: No I have a problem I have a simulation, but I lost my .cpt file and .edr file. I don’t have my .cpt file from 500 ns (but I have .cpt file from 400 ns), I try to rerun from 400 ns, but it gives my a little bit different final structure, because I don’t compute on the same computer, so I want to try rerun from 500 ns last frame, with .trr file in which I have velocities, forces and energies. Is it possible and how to do it? What should I do? ---
**Author:** ![pjohansson](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pjohansson/32/316_2.png) [@pjohansson](https://gromacs.bioexcel.eu/u/pjohansson)\ **Post date:** [March 23, 2021, 7:08am UTC](https://gromacs.bioexcel.eu/t/is-it-possible-to-continue-simulation-without-cpt-file-when-i-have-trr-and-xtc-file/1796/2 "2021-03-23T07:08:39Z")
Hello, you can call `grompp` with your trajectory as input with the `-t [.trrfile]` flag, along with the rest of your parameters. This generates a `.tpr` file with the last frame from the trajectory as a starting point (unless you generate new velocities in your `.mdp` file). Regards, Petter ---
**Author:** ![JakubH](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@JakubH](https://gromacs.bioexcel.eu/u/JakubH)\ **Post date:** [March 23, 2021, 11:44am UTC](https://gromacs.bioexcel.eu/t/is-it-possible-to-continue-simulation-without-cpt-file-when-i-have-trr-and-xtc-file/1796/3 "2021-03-23T11:44:31Z")
pjohansson thank you so much for responding. I try but it is not working. I don’t know why it is not working. I call grompp gmx grompp -f eq2.mdp -c MGDG\_last\_frame\_500ns.gro -t eq2.part0006.trr -p system\_mgdg.top -o eq2\_continuation.tpr Then in my terminal I have :-) GROMACS - gmx grompp, 2020.2 (-: GROMACS: gmx grompp, version 2020.2 Executable: /usr/local/gromacs2020\_2/bin/gmx Data prefix: /usr/local/gromacs2020\_2 Working dir: /media/jakub/Maxtor1/MGDG\_trzy\_warstwy\_15\_11\_2020/400\_500ns Command line: gmx grompp -f eq2.mdp -c MGDG\_last\_frame\_500ns.gro -t eq2.part0006.trr -p system\_mgdg.top -o eq2\_continuation.tpr Ignoring obsolete mdp entry ‘title’ Ignoring obsolete mdp entry ‘cpp’ Ignoring obsolete mdp entry ‘ns\_type’ Replacing old mdp entry ‘nstxtcout’ by ‘nstxout-compressed’ NOTE 1 [file eq2.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 Setting the LD random seed to -304252109 Generated 190 of the 190 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 190 of the 190 1-4 parameter combinations Excluding 3 bonded neighbours molecule type ‘mgdg’ turning H bonds into constraints… Excluding 2 bonded neighbours molecule type ‘SOL’ turning H bonds into constraints… Analysing residue names: There are: 32400 Other residues There are: 121500 Water residues Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups… Number of degrees of freedom in T-Coupling group Water is 728999.31 Number of degrees of freedom in T-Coupling group non-Water is 2535297.75 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 353 K Calculated rlist for 1x1 atom pair-list as 1.020 nm, buffer size 0.020 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory trr version: GMX\_trn\_file (single precision) Last frame 100 time 500000.000 Using frame at t = 500000 ps Starting time for run is 0 ps Calculating fourier grid dimensions for X Y Z Using a fourier grid of 256x384x160, spacing 0.095 0.099 0.097 Estimate for the relative computational load of the PME mesh part: 0.35 NOTE 2 [file eq2.mdp]: This run will generate roughly 1708892 Mb of data There were 2 notes Back Off! I just backed up eq2\_continuation.tpr to ./#eq2\_continuation.tpr.15# GROMACS reminds you: “But I always say, one’s company, two’s a crowd, and three’s a party.” (Andy Warhol) This is my mdp file title = MD equilibration; tinit = 0 cpp = /lib/cpp ; constraints = hbonds constraint\_algorithm = lincs ; integrator = md dt = 0.002 ; nsteps = 250500000 ; nstcomm = 100 ; comm\_mode = linear continuation = yes ; ; output nstxout = 500000 ; nstvout = 500000 ; nstxtcout = 1000 ; nstfout = 500000 ; nstlog = 1000 ; nstenergy = 1000 ; nstcalcenergy = 100 cutoff-scheme = Verlet ; ns\_type = grid nstlist = 10 ; pbc = xyz coulombtype = PME rvdw = 1.0 ; rlist = 1.0 rcoulomb = 1.0 fourierspacing = 0.1 ; pme\_order = 5 ; ewald\_rtol = 1e-5 ; temperature coupling tcoupl = nose-hoover tc-grps = water non-water tau\_t = 0.5 0.5 ; ref\_t = 353 353 ; pressure Pcoupl = parrinello-rahman ; parrinello-rahman/no/berendsen Pcoupltype = anisotropic ; tau\_p = 5.0 compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0 ref\_p = 1 1 1 0.0 0.0 0.0 ; When I start mdrun I have starting mdrun ‘450 mgdg molecules in water’ 250500000 steps, 501000.0 ps. step 0 starting mdrun ‘450 mgdg molecules in water’ 250500000 steps, 501000.0 ps. step 0 ---
**Author:** ![pjohansson](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/pjohansson/32/316_2.png) [@pjohansson](https://gromacs.bioexcel.eu/u/pjohansson)\ **Post date:** [March 24, 2021, 6:27am UTC](https://gromacs.bioexcel.eu/t/is-it-possible-to-continue-simulation-without-cpt-file-when-i-have-trr-and-xtc-file/1796/4 "2021-03-24T06:27:56Z")
It seems to me like it works. It picks up the last frame here: > [@JakubH](#): > > Last frame 100 time 500000.000 > Using frame at t = 500000 ps > Starting time for run is 0 ps If you want t0 (which is independent of `-t`) to be 500ns you need to modify the `init-step` variable to match it. Petter ---
**Author:** ![JakubH](https://avatars.discourse-cdn.com/v4/letter/j/df788c/32.png) [@JakubH](https://gromacs.bioexcel.eu/u/JakubH)\ **Post date:** [March 27, 2021, 2:04pm UTC](https://gromacs.bioexcel.eu/t/is-it-possible-to-continue-simulation-without-cpt-file-when-i-have-trr-and-xtc-file/1796/5 "2021-03-27T14:04:49Z")
Thank you so much!