# Extending/Append metadynamics simulation

**URL:** <https://gromacs.bioexcel.eu/t/extending-append-metadynamics-simulation/10921>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [December 30, 2024, 7:03am UTC](https://gromacs.bioexcel.eu/t/extending-append-metadynamics-simulation/10921 "2024-12-30T07:03:55Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![gurpreet](https://avatars.discourse-cdn.com/v4/letter/g/fbc32d/32.png) [@gurpreet](https://gromacs.bioexcel.eu/u/gurpreet)\
**Post date:** [December 30, 2024, 7:03am UTC](https://gromacs.bioexcel.eu/t/extending-append-metadynamics-simulation/10921/1 "2024-12-30T07:03:55Z")

</div>

GROMACS version:2023  
GROMACS modification: Yes  
Plumed 2-2.9.0

I have run a metadynamics simulation for my protein complex for 100 ns and generated the free energy surface (FES). I want to extend the simulation for another 100 ns.  
The output files I have are: COLVAR, confout.gro, ener.edr, HILLS, md.log, state.cpt and traj\_comp.xtc.  
Would really appreciate the guidance on how to proceed with extending/append the simulation?

---

<div class="post-metadata">

**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\
**Post date:** [December 30, 2024, 9:27am UTC](https://gromacs.bioexcel.eu/t/extending-append-metadynamics-simulation/10921/2 "2024-12-30T09:27:12Z")

</div>

Dear @gurpreet

This is a PLUMED more than a GROMACS question, as you have patched GROMACS and are using external functionalities.

In general, to continue a simulation, you have to provide the checkpoint (`.cpt`) file to `mdrun` with the flag `-cpi`. Since you want to continue the simulation with also PLUMED, you will have to pass again the flag and corresponding file, something like `-plumed plumed.dat`. This last file is the one where you defined what PLUMED is supposed to be doing and it is where you have to specify the keywords to restart the simulations. Take a look at their manual, [here](https://www.plumed.org/doc-v2.9/user-doc/html/_m_e_t_a_d.html) if you are doing metadynamics. There is going to be the keyword RESTART that has to be put somewhere plus some files to point to, probably.

Overall, the command will look like this more or less

```auto
gmx mdrun [...] -s prod.tpr -cpi prod.cpt -plumed plumed.dat

```

where the `plumed.dat` file is the updated one for the restart. I highly suggest you to backup the directory with the run files so that if the restart fails you do not modify/corrupt the outcome of the previous run!