Hi everyone, I have a query to ask regarding molecular dynamic simulation by using Gromacs. When the running simulation was accidentally stopped, and re-run, should I need to type any command to combine the .gro file or any file?
Actually, I had run some simulation. The problem was, some of the graphs gave only 30ns (or less than 50ns) while, I am running for 50ns Md simulation. I have checked the .log file and found that the simulation was finished running for 50ns. Here, I attached the rmsd picture and the .log file for your reference.
Thank you.
To continue the your terminated simulation, you can use given below command to continue your simulation.
gmx mdrun -v -s md.tpr -cpi md.cpt -noappend or append
for the details you can check here
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
Why your simulation accidentally stopped?, please try to get the region. Did u check the rmsd.xvg text file?
Regards,
Nandan
Thanks Nandan.
Actually, my simulation stopped due to the electrical breakdown. I have successfully used that command to continue my simulation. The thing is, the simulation supposed to have 50ns Rmsd graph. But, the result only shows 30ns graph. I doubt that this might be related to the stopped simulation. Maybe instead of typing this command (gmx mdrun -v -s md.tpr -cpi md.cpt -noappend or append), there is another step that I should do to obtain the result.
By the way, thanks for replying.
Did you merge both trajectories before calculating RMSD.
You can use
gmx trjcat -f 1.trr 2.trr -o final.trr
Thanks a lot Nandan Kumar!
I have tried to concatenate all the multiple trajectory files and it works. Thanks again for your help.
- Badges
- Science topic