Mark, i want to know which water atoms stay within a cut off to protein atom. ie i need the duration at which a water resides on the protein atoms. so for that i need the whole 5ns frames because am looking for water molecules which reside more than 50% of time.
Thanks On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham <[email protected]>wrote: > On 29/02/2012 6:01 PM, aiswarya pawar wrote: > > Mark, > > Right now am computing distance between each protein atom against all > water atoms, > > > That's expensive. mdrun goes to great lengths to speed up computing > billions of distances. > > which is taking too long for 5ns run. i cant reduce the frames > > > Yes you can. Even if you think you need data from every frame, you > probably don't because they're correlated with each other, and at the very > least you can do a pilot study on a frame every 100ps or every nanosecond > before committing to one on all the frames. > > > either the number of water atoms. So is there any alternate. > > > You are not likely to get a better solution if you only describe your > attempt, rather than describe the objective. Asking "how do I hammer > harder?" if you're hammering a screw makes it impossible to get the correct > solution "Use a screwdriver". > > Mark > > > Thanks > > On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham <[email protected]>wrote: > >> On 29/02/2012 5:17 PM, aiswarya pawar wrote: >> >> Dear all, >> >> Am running g_mindist on large number of atoms, i would like to know >> whether i can run this on more than one processors say 8 processors to >> speed up the task? >> >> >> No. If it will take too long, you need to reduce your number of frames >> (trjconv), or the number of atoms (also trjconv), or some such. >> >> Mark >> >> >> and will this effect the output in anyways. >> >> Thanks, >> >> -- >> Aiswarya B Pawar >> >> >> >> >> >> >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Aiswarya B Pawar > > Project Assistant, > Bioinformatics Dept, > Indian Institute of Science > Bangalore > > > > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Aiswarya B Pawar Project Assistant, Bioinformatics Dept, Indian Institute of Science Bangalore
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