Extension of the run at production stage

User discussions
1

GROMACS version:2022.2
GROMACS modification: No
@jalemkul

I ran production-1 gmx mdrun -v -noappend -deffnm pro1 -ntmpi 32 for 30 ns (nsteps=15000000, dt=0.002), which was executed successfully in 20 Hrs. i.e. (1.5ns/hour)

Now I want to extend the run by 10 ns (nsteps=5000000, dt=0.002) and used the following commands

gmx convert-tpr -s pro1.tpr -o pro2.tpr -extend 5000000
gmx mdrun -v -noappend -cpi pro1.cpt -deffnm pro2 -ntmpi 32

Not sure why isn’t it completed even after 12 Hrs (Using same machine), also it has executed more steps than 5000000.

Please find the log below

gmx convert-tpr -s pro1.tpr -o pro2.tpr -extend 5000000

Reading file pro1.tpr, VERSION 2022.2 (single precision)
Input file:
  Run start step                                     0
  Run start time                                     0 ps
  Step to be made during run                  15000000
  Runtime for the run                            30000 ps
  Run end step                                15000000
  Run end time                                   30000 ps

Extending remaining runtime by 5e+06 ps

Output file:
  Run start step                                     0
  Run start time                                     0 ps
  Step to be made during run                2515000000
  Runtime for the run                         5.03e+06 ps
  Run end step                              2515000000
  Run end time                                5.03e+06 ps

  gmx mdrun -v -noappend -cpi pro1.cpt -deffnm pro2 -ntmpi 32

  **26275700 will finish Sat Mar 11 19:12:14 2023**

Total steps should be 15000000+5000000=> 20000000, but it has exceeded way beyond and continuing it.
Why so? Is it obvious or I have made some mistake?

Thanks

2

The value of -extend is time in ps, not a number of steps. You’re asking for an extension of 5 μs, not 5 million steps.

3

Thanks.