Mansi .. DId you read my question..?

My apologies, Sir. I misunderstood your question. Unfortunately, I'm not able to help with this right now

I might be wrong, but personally I do not think you can. You can generate a new .tpr file pointing at the last frame of the trajectory, and continue from there, although that is not going to be an exact continuation. For a proper continuation, that is, the -cpi flag of mdrun, you need a .cpt file. I do not think you can generate/recover it from the other files are from my understanding the .cpt is a binary that keeps the last velocities, forces, barostat/thermostat states etc.

I hope I am wrong and someone comes out with a solution, as sometimes I also need to continue from a corrupted .cpt.

Nicola Piasentin Thanks a lot for your suggestion..I totally agree with your remarks..Could you please how can I generate a new tpr file using the last frame of the trajectory? Shoul I dump or is there any other way to work around? I have a very large system..

Dear Budheswar Dehury

Yes, I would dump the last frame of the trajectory as a .gro file and use it in the gmx grompp passage, something like

gmx grompp -f old_mdp_file.mdp -c last_frame.gro -p topology.top -n index.ndx -o extended_run.tpr

and run the new tpr. It is not going to be an exact continuation but I would say that it is better than nothing!

Nicola Piasentin Thanks a lot for your time and input. The previous MD run which stopped abruptly was an extended version of a previous MD run. So I bleieve I need to change the

init-step ... in the mdp file for generating the new tpr file before running the production MD? Kindly provide your feedback.

Thanks and Regards

Budheswar

Dear Budheswar Dehury

You can read about that parameter in the mdp file here

https://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-init-step

Personally, I have never used it. If yours is just a plain MD simulation, I would let it undefined, i.e. 0.

You can try this out. However, I don't know if this will work.

1. You must ensure that you have the necessary input files of your previous simulation, which include the topology file (.top), the last coordinate file (.gro), and the trajectory file (.xtc).

2. By using the the gmx grompp command, prepare a new .tpr file. Specify the last frame of your trajectory as a starting point.

Possible Syntax:

gmx grompp -f md.mdp -c last_frame.gro -p topol.top -o new_simulation_file.tpr

3. Now, the last_frame.gro file can be used as the coordinate file that corresponds to the last frame of the previously undertaken simulation.

4. Now, using the 'gmx mdrun' command, start your MD Simulation. Ensure that you are appending to the existing trajectory files.

Possible Syntax:

gmx mdrun -deffnm new_simulation_file -append

Here, the append command should allow you to continue writing on the existing output file.