Hi gromacs users,
I am running 50 ns seconds MD job in 5 differents parts like wise 10, 10 ns. How can I set enviroment or command through which I can run in single command. I have used gmx convert-tpr command but it requires extend command after every 10 ns time. Is there any option in gromacs that I can run 50 ns job which creates diferent trajectories and gro files after every 10, 10 ns run in single command.
Thanks in advance.
Regards,
Abid Ali Channa
Uni of Karachi. Pakistan
Dear Abid!
I'm not sure that I understand your question correctly, but...
You can run your 50ns MD trajectory in one part and after this you can devide all your trajectory files (.gro, .trr., etc) as you wish using gmx trjconv command.
Something like this:
gmx trjconv -f [] -b (first frame in ps) -e (last frame) ...
Dear Kirill E Medvedev!
Thanks for your suggestion. My query is that I want to run 50 ns job in parts. I want to visualize my job every 10 ns . Because I want to all output files like .xtc, .gro, .edr, .log, .trr, .trj after every 10 ns run. Because my final .gro file is formed after 50 ns job. I want to .gro files of every 10 ns job not 50 ns in total 50 ns Job.
Thanks again for your reply.
Dear Abid!
I'm not sure that it is possible to do in single command.
I can only suggest you to use Gromacs checkpoint files:
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
In this case you can make five 10 ns runs with all output files and join these runs using checkpoint files.
- Badges
- Science topic
- Similar topics
- Chemistry
- Biochemistry
- Biomolecules