Hi,<br><br>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).
<br><br>Thanks again!<br>Corina<br><br><div><span class="gmail_quote">On 6/26/07, <b class="gmail_sendername">Martin Höfling</b> <<a href="mailto:martin.hoefling@gmx.de">martin.hoefling@gmx.de</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Am Montag, 25. Juni 2007 schrieb Corina Stratan:<br><br>Hi Cornia,<br><br>these are my experiences, so others might differ from mine:<br><br>> 1) Which is the typical size of the input/output files for Gromacs<br>> programs? The ones included in the tutorial are below 50K; are the files
<br>> larger in "real" situations? And if yes, is there any place we can find<br>> some larger test files?<br><br>If you consider the PDB or binary topology (tpr) file as input, you are in the<br>order of 100k-1M. This size mainly depends on the size of your system.
<br>Parameters contribute pretty much nothing to the input size.<br>Same with the output: it depends what you're interested on. For some<br>applications, a single (uncompressed) trajectory grew to 100G, but typically<br>
it's at least one magnitude below. If you want a _large_ input, you can just<br>solvate a protein in a large water box.<br><br>> 2) Which would be the typical running time of an mdrun simulation? (or put<br>> it another way, is the runtime usually significant -
i.e., more than a few<br>> minutes?)<br><br>This depends on what you're interested in. For parameter studies, where you<br>need hundreds or thousands of simulations, you usually use small systems.<br>Runtime is in the order of minutes to hours, sometimes in days. (on a single
<br>processor)<br>For other experiments, simulation time can grow to 3 month for one simulation<br>on a single processor)<br><br>> 3) Are the jobs usually run in batch? And if yes, do the batches contain a<br>> single program, run with different input files, or multiple programs?
<br><br>Normally, you run "mdrun" together with different input files. What do you<br>mean by multiple programs? Batch scripts sometimes contain preprocessing<br>(with different programs) but this is executed in serial and my guess would
<br>be that mdrun takes 99.99% of cpu time for most applications. If you consider<br>MPI processes on different machines as individual programs, then there can be<br>a lot, depending on parallelization level used.<br><br>
Best<br> Martin<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Murphy's law current revision:<br>Any thing that can go wrong, HAS Already Gone Wrong! You just haven't been notified.