[gmx-users] A few general questions on Gromacs

Corina Stratan corina.stratan at gmail.com
Tue Jun 26 15:30:02 CEST 2007


I would like to thank you and David for the answers. By "multiple programs",
I meant batch scripts that contain other preprocessing/postprocessing
programs besides mdrun  (like grompp, pdb2gmx,...) - so this would be a case
in which the processing is done in multiple steps. I asked this because
we're especially interested in multi-step processes (workflows); and in the
Gromacs tutorials most of the examples are like this (some other programs
are invoked before and after mdrun).

Thanks again!

On 6/26/07, Martin Höfling <martin.hoefling at gmx.de> wrote:
> Am Montag, 25. Juni 2007 schrieb Corina Stratan:
> Hi Cornia,
> these are my experiences, so others might differ from mine:
> > 1) Which is the typical size of the input/output files for Gromacs
> > programs? The ones included in the tutorial are below 50K; are the files
> > larger in "real" situations? And if yes, is there any place we can find
> > some larger test files?
> If you consider the PDB or binary topology (tpr) file as input, you are in
> the
> order of 100k-1M. This size mainly depends on the size of your system.
> Parameters contribute pretty much nothing to the input size.
> Same with the output: it depends what you're interested on. For some
> applications, a single (uncompressed) trajectory grew to 100G, but
> typically
> it's at least one magnitude below. If you want a _large_ input, you can
> just
> solvate a protein in a large water box.
> > 2) Which would be the typical running time of an mdrun simulation? (or
> put
> > it another way, is the runtime usually significant - i.e., more than a
> few
> > minutes?)
> This depends on what you're interested in. For parameter studies, where
> you
> need hundreds or thousands of simulations, you usually use small systems.
> Runtime is in the order of minutes to hours, sometimes in days. (on a
> single
> processor)
> For other experiments, simulation time can grow to 3 month for one
> simulation
> on a single processor)
> > 3) Are the jobs usually run in batch? And if yes, do the batches contain
> a
> > single program, run with different input files, or multiple programs?
> Normally, you run "mdrun" together with different input files. What do you
> mean by multiple programs? Batch scripts sometimes contain preprocessing
> (with different programs) but this is executed in serial and my guess
> would
> be that mdrun takes 99.99% of cpu time for most applications. If you
> consider
> MPI processes on different machines as individual programs, then there can
> be
> a lot, depending on parallelization level used.
> Best
>         Martin
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