Can I change the 0.99 to e.g. 0.95 for -maxh?

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1

GROMACS version:2020.4
GROMACS modification: No
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With option -maxh a simulation is terminated and a checkpoint file is written at the first neighbor search step where the run time exceeds -maxh *0.99 hours.

Can I change the 0.99 to e.g. 0.95 so as to allow sufficient time for writing the cpi files?

I am doing REMD, which needs to write dozens of cpi files. In one of my log files, there is only

Writing checkpoint, step 92601 at Sun Feb 28 08:32:18 2021

at the end, without the performance report like

   Core t (s)   Wall t (s)        (%)
   Time:    14296.224     3574.057      400.0
             59:34
     (ns/day)    (hour/ns)
Performance:        4.480        5.358
Finished mdrun on rank 0 Sun Feb 28 00:47:33 2021

So I think, the program does not have suffcient time to output the performance report. Is that correct that, with flag -maxh 1, the performance report should ideally be written at the end of the log file?

If I give more time, e.g. 5% instead of 1%, the program should elegantly terminate the run, write all the cpi file, and output the performance report?

2

Yes, you should get the performance report. So you run does not seem to reach the next ns step. We the value 0.99 with a typical time of 24 hours in mind, which seems to be unproblematic. Here you use 1 hour, which might leave too little time. The solution is simply to supply hours*0.95 to the -maxh option.

3

Thank you. Do you mean the exact command should be -maxh 0.95 or -maxh 1*0.95 ?

4

-maxh 0.95 would set it to 57 minutes, you should set it to 0.95 times the allocated job time (in hours). Eg. -maxh 3.8 for a 4 hour job. (Edit: to be precise, this will end the simulation at 0.99 * 0.95 * hours, adjust appropriately if you need to)

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5

But I am still confused. The manual says:

-maxh (-1)
Terminate after 0.99 times this time (hours)

This means, if -maxh 0.95 is used, it will terminates 0.99*0.95 = 0.9405 hour. I feel 0.99 has been fixed.

6

Sure 0.99 has been fixed in the code. So if you want exaclty 0.95 hours (plus the times it takes mdrun to get to the next ns step), supply -maxh 0.959595959596

7

Thank you, now I fully got the usage.