# Problems in restarting simulation **URL:** \ **Category:** User discussions\ **Created:** [July 8, 2020, 8:23pm UTC](https://gromacs.bioexcel.eu/t/problems-in-restarting-simulation/447 "2020-07-08T20:23:44Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![qweqwe](https://avatars.discourse-cdn.com/v4/letter/q/8e7dd6/32.png) [@qweqwe](https://gromacs.bioexcel.eu/u/qweqwe)\ **Post date:** [July 8, 2020, 8:23pm UTC](https://gromacs.bioexcel.eu/t/problems-in-restarting-simulation/447/1 "2020-07-08T20:23:44Z")
GROMACS version: 2016.3 GROMACS modification: Yes/No Here post your question Hi everyone, I am restarting my simulation from the last point in my trajectory. As I want to sample steps with more frequency for the simulation after restart I have to supply a new mdp file and use these commands as mentioned in the manual:: gmx\_mpi grompp -f tmp.mdp -p water.top -t c.cpt -c confout.gro -o new.tpr gmx\_mpi mdrun -s new.tpr -cpi c.cpt -ntomp 1 -v -deffnm cnt -reprod -noappend The simulation runs to infinity after mdrun and the output on the screen is – WARNING: This run will generate roughly 641868500016085376 Mb of data 300 steps, infinite ps (continuing from step 1000000, 1000.0 ps). However supplying mdrun with only tpr file and without cpt file helps prevent this and runs only for the desired steps. Output is -: 300 steps, 0.3 ps. I am storing data at 1 fs interval, earlier I was storing it every 100 fs and I am using Gromacs/2016.3 . Running gmx check on the c.cpt file I obtain Last frame -1 time 1000.000 Item #frames Timestep (ps) Step 1 Time 1 Lambda 1 Coords 1 Velocities 1 Forces 0 Box 1 What sequence of steps should I use in order to sample my restart simulation at a different frequency ? Thnx everyone ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [July 8, 2020, 10:04pm UTC](https://gromacs.bioexcel.eu/t/problems-in-restarting-simulation/447/2 "2020-07-08T22:04:29Z")
[http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart](http://manual.gromacs.org/documentation/current/user-guide/managing-simulations.html#changing-mdp-options-for-a-restart) ---
**Author:** ![qweqwe](https://avatars.discourse-cdn.com/v4/letter/q/8e7dd6/32.png) [@qweqwe](https://gromacs.bioexcel.eu/u/qweqwe)\ **Post date:** [July 9, 2020, 11:03am UTC](https://gromacs.bioexcel.eu/t/problems-in-restarting-simulation/447/3 "2020-07-09T11:03:47Z")
I had gone through this and used the commands mentioned in “Changing mdp options for a restart” as mentioned above but still could not figure out why i am running into an infinite simulation . How should i use the checkpoint file with mdrun ? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [July 9, 2020, 12:09pm UTC](https://gromacs.bioexcel.eu/t/problems-in-restarting-simulation/447/4 "2020-07-09T12:09:41Z")
The infinite time probably comes from failing to set `tinit` as the information in the link notes. Without your `.mdp` file, we can’t be sure. The syntax for `grompp` and `mdrun` is exactly as shown in that link. That’s how you make use of the checkpoint file. ---
**Author:** ![qweqwe](https://avatars.discourse-cdn.com/v4/letter/q/8e7dd6/32.png) [@qweqwe](https://gromacs.bioexcel.eu/u/qweqwe)\ **Post date:** [July 11, 2020, 7:37am UTC](https://gromacs.bioexcel.eu/t/problems-in-restarting-simulation/447/5 "2020-07-11T07:37:35Z")
Thnx @jalemkul , @Dr_DBW . According to the above replies , I tried all possible combinations to restart my simulation from 1000 ps to 1000.3 ps ( 1000000 to 1000300 steps). 1.nsteps = 300 tinit = 0 ps init-step = 0 OUTPUT --\> 300 steps, infinite ps (continuing from step 1000000, 1000.0 ps). 0th step on log file --\> Step Time 1000000 1000.00000 1. nsteps = 300 tinit = 1000 ps init-step = 0 OUTPUT --\> 300 steps, infinite ps (continuing from step 1000000, 1000.0 ps). 0th step on log file --\> Step Time 1000000 2000.00000 1. nsteps = 300 tinit = 0 ps init-step = 1000000 OUTPUT --\> 1000300 steps, 1000.3 ps (continuing from step 1000000, 1000.0 ps). 0th step on log file --\> Step Time 1000000 1000.00000 1. nsteps = 300 tinit = 1000 ps init-step = 1000000 OUTPUT --\> 1000300 steps, 1000.3 ps (continuing from step 1000000, 1000.0 ps). 0th step on log file --\> Step Time 1000000 2000.00000 The 3rd simulation began and ended at the desired time and correct number of steps. Is this the correct way to restart the simulation mentioning both the beginning time and the number of steps ? The mdp file is pasted below --\> ; Define can be used to control processes define = -DPOSRES ; Parameters describing what to do, when to stop and what to save integrator = md-vv ; Algorithm nsteps = 300 ; Maximum number of (minimization) steps to perform(10 ns) init-step = 1000000 ; dt = 0.001 ; time step(1 fs or .001 ps) nstfout = 1 ; nstxout = 1 ; nstvout = 1 ; nstlog = 1 ; nstenergy = 1 ; Write energies to disk every nstenergy steps nstcalcenergy = 10 ; nstxout-compressed = 1 ; energygrps = SOL ; Which energy group(s) to write to disk ;NVE nstcomm = 10 ; frequency for center of mass motion removal comm-mode = Linear ; remove com translation and rotation around com comm-grps = SOL ; group(s) for center of mass motion removal ;SEARCHLIST cutoff-scheme = Verlet ; nstlist = 10 ; Frequency to update the neighbor list(default) ns\_type = grid ; Method to determine neighbor list (simple, grid) pbc = xyz ; verlet-buffer-tolerance = 0.005 ; maximum error for pair interactions per particle(default) ;USING LJ-PME coulombtype = PME vdwtype = PME rlist = 1.4 rvdw = 1.4 rcoulomb = 1.4 fourierspacing = 0.12 pme-order = 4 ewald-rtol-lj = 0.001 lj-pme-comb-rule = geometric DispCorr = Ener ;BOND CONSTRAINTS continuation = yes ; Continue NVT after the box has been resized constraints = h-bonds ; Bond types to replace by constraints constraint\_algorithm = shake ; ;Velocity generation gen-vel = no ; gen-temp = 298 ; Thnx everyone ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [July 13, 2020, 11:11am UTC](https://gromacs.bioexcel.eu/t/problems-in-restarting-simulation/447/6 "2020-07-13T11:11:20Z")
As noted at [http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-init-step](http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-init-step) `t = tinit + dt * (init-step + i)` to get the correct starting time of `t=1000` for your extension you have to set `tinit=0`, `init-step=1000000`, `dt=0.001`.