[gmx-users] mdrun -nsteps

[Sabine Reisser]

Alright, thanks!

Am 17.02.2015 13:48, schrieb Mark Abraham:
> Hi,
>
> The second call to mdrun will run 10000 steps if it can. Whether that is a
> continuation or not depends what checkpoint mdrun finds, etc.
>
> gmx mdrun -h says
>
> "-nsteps Run this number of steps, overrides .mdp option"
>
> This is true, from the point of view of the next MD simulation part, which
> is what mdrun does. That this part is just one piece of a bigger picture
> isn't something mdrun needs to help you manage, I think.
>
> Using the word "append" would be ambiguous, because gmx mdrun -append
> refers to running some number of steps and concatenating the output files
> (or not, with -noappend). "Continue" doesn't fully work either, because it
> implies the existence of a previous simulation part.
>
> The main alternative would be defining -nsteps as "do this total number of
> steps, starting from the checkpoint (if any)." This isn't very usable
> unless you know for sure what is in your checkpoint. The current meaning
> for -nsteps means that it is easy to write a job submission script e.g. for
> 2 hours doing 50,000 more steps - which is awkward otherwise.
>
> Cheers,
>
> Mark
>
>
> On Tue, Feb 17, 2015 at 12:10 PM, Sabine Reisser <sabine.reisser at kit.edu>
> wrote:
>
>> Hi,
>>
>> just to be sure: is it intended, that the -nsteps option in mdrun (which
>> is a great feature in general!) actually appends the given number of steps
>> rather than overriding the mdp option?
>> This is what I do:
>> - grompp with mdp file with 5000 steps
>> - mdrun
>> - mdrun -nsteps 10000 steps
>>
>> The second mdrun runs until 15000 steps, not 10000 steps. Is this
>> intended? If yes, the option description is somewhat misleading.
>>
>> Cheers
>> Sabine
>>
>>
>> --
>> Dipl. Phys. Sabine Reißer
>> Karlsruhe Institute of Technology (KIT)
>> Institute of Physical Chemistry
>>
>> Phone +49 (0) 721 / 608-45070
>>
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-- 
Dipl. Phys. Sabine Reißer
Karlsruhe Institute of Technology (KIT)
Institute of Physical Chemistry

Phone +49 (0) 721 / 608-45070