From marcus.lundbe from gmail.com Mon Feb 12 12:17:34 2007 From: marcus.lundbe from gmail.com (marcus.lundbe@gmail.com) Date: Mon Feb 12 20:50:04 2007 Subject: [Molecular-modelling] computation time for different molecules Message-ID: Hi, I'm working on optimizing DOCK6 on a massively parallel computer, and we're running into a problem with scaling. We'd like to find a way to estimate the time it takes to dock various ligands in a query. This information can be used to produce an ordering that allows all the compute nodes work efficiently without a lot of idle time. We have a start already: the larger the molecule, the longer the calculation, in general. This rule only results in limited success. There is some other feature of the molecule or computation that causes some small molecules to take an exorbitant amount of time, and some larger molecules are finished very quickly. Does anyone know of any similar work being done? Any suggestions or comments are welcome. (Also, is there another usenet group that might be a better venue to ask in?) -Marcus Lundberg From engelbert_buxbaum from hotmail.com Tue Feb 20 07:21:01 2007 From: engelbert_buxbaum from hotmail.com (Dr Engelbert Buxbaum) Date: Tue Feb 20 12:36:54 2007 Subject: [Molecular-modelling] Re: computation time for different molecules References: Message-ID: marcus.lundbe@gmail.com wrote: > We have a start already: the larger the molecule, the longer the > calculation, in general. This rule only results in limited success. > There is some other feature of the molecule or computation that causes > some small molecules to take an exorbitant amount of time, and some > larger molecules are finished very quickly. Try bionet.biology.computational, people hanging out there may be able to help.