Hi,
I have run a simulation of 200 ns. Now I realized that I wanted to run it till 500 ns in total to explore more dynamics. Instead of extending the simulation by gmx convert-tpr command, I took the final frame of my 200 ns trajectory file and take that as starting configuration for my next 300 ns run.
I changed in my .mdp option the time from 200 ns to 300 ns and put continuation = yes so that it continues from the last frame where it stopped and then again run gmx grompp and gmx mdrun command.
Can anyone tell me if it is the correct method to extend the simulation?
Thanks!
Neither you should do what you suggested above nor you require to use gmx-convert. Instead, you need to use the checkpoint file ".cpi" generated from your previous MD run. You can even omit modifying your ".mdp" file if you just use -until option according to the link attached below.
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
https://www.researchgate.net/post/How_does_one_extend_the_protein_simulation_in_Gromacs_and_check_the_total_time_of_the_MD
In the trajectory file the time for the simulation is recorded. So this will not start another 300 ns but continue the 200 ns simulation and extend it to 300 ns.
You should, as Vishal Pandya has stated just now, use the checkpoint '.cpi' as the initial structure and merge it with the .mdp file.
you can run simulation using .gro output but note do not generate velocity again. by means of a trjcat command you can merge two trajectory file and do further analysis.
No. Particularly if you are interested in dynamic continuity. gro files have low precision (normally 3 places of decimal), hence the coordinate and velocity values would not be exactly same as the high precision ones due to truncation. It is highly recommended to use the check-point (.cpt) files as suggested by others already.
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