Re: [gmx-users] using more processors for g_mindist
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 mark.abra...@anu.edu.auwrote: 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 mark.abra...@anu.edu.auwrote: 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] using more processors for g_mindist
On 29/02/2012 7:21 PM, aiswarya pawar wrote: Mark, i want to know which water atoms stay within a cut off to protein atom. OK, but as you will read in g_mindist -h, it will count such atoms and not identify which they were... ie i need the duration at which a water resides on the protein atoms. ... and identity of the atoms is needed for measuring duration of contact. g_dist does something like this, and reading g_mindist -h should have prompted you to find this out. Otherwise, you will have to construct an index group for each water molecule, and script a loop to examine each water molecule separately using some tool that observes what you really want to measure. so for that i need the whole 5ns frames because am looking for water molecules which reside more than 50% of time. You also need to be clear about whether you care about continuous contact. Does a water molecule that oscillates at a distance around the cutoff reside about 50% of the time? You still don't need high time resolution for testing whether this analysis might give you the information you want. The water molecules that are in contact for more than 50% of the time (continuous or not) will show up in 5 snapsnots spaced every nanosecond. 5000 snapshots every picosecond is better, but not if you can't afford to wait for it. Mark Thanks On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au 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 mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au 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 gmx-users@gromacs.org mailto:gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. 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 gmx-users@gromacs.org mailto:gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] using more processors for g_mindist
Mark, In the g_mindist output data gives which atom was within cutoff to protein atom ie the output file of g_mindist 5.00e+02 518 42680 5.01e+02 518 20942 5.02e+02 518 67844 5.03e+02 518 5984 5.04e+02 518 67844 5.05e+02 518 5984 5.06e+02 518 30116 5.07e+02 518 67844 5.08e+02 518 32957 5.09e+02 518 67844 5.10e+02 518 19610 5.11e+02 518 19610 5.12e+02 518 22895 5.13e+02 518 30116 5.14e+02 518 19610 5.15e+02 518 22895 5.16e+02 518 13628 5.17e+02 518 5984 2nd column is the protein atom and the 3rd column the water atom. if iam doing g_dist how is it possible to know the which water molecule has to be considered for the distance calculations ie should i compute the distance between one protein atom against all the water within the cut off individually? Thanks On Wed, Feb 29, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.auwrote: On 29/02/2012 7:21 PM, aiswarya pawar wrote: Mark, i want to know which water atoms stay within a cut off to protein atom. OK, but as you will read in g_mindist -h, it will count such atoms and not identify which they were... ie i need the duration at which a water resides on the protein atoms. ... and identity of the atoms is needed for measuring duration of contact. g_dist does something like this, and reading g_mindist -h should have prompted you to find this out. Otherwise, you will have to construct an index group for each water molecule, and script a loop to examine each water molecule separately using some tool that observes what you really want to measure. so for that i need the whole 5ns frames because am looking for water molecules which reside more than 50% of time. You also need to be clear about whether you care about continuous contact. Does a water molecule that oscillates at a distance around the cutoff reside about 50% of the time? You still don't need high time resolution for testing whether this analysis might give you the information you want. The water molecules that are in contact for more than 50% of the time (continuous or not) will show up in 5 snapsnots spaced every nanosecond. 5000 snapshots every picosecond is better, but not if you can't afford to wait for it. Mark Thanks On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham mark.abra...@anu.edu.auwrote: 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 mark.abra...@anu.edu.auwrote: 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read
Re: [gmx-users] using more processors for g_mindist
On 29/02/2012 9:05 PM, aiswarya pawar wrote: Mark, In the g_mindist output data gives which atom was within cutoff to protein atom ie the output file of g_mindist What makes you think there is only one atom satisfying that cutoff? 5.00e+02 518 42680 5.01e+02 518 20942 5.02e+02 518 67844 5.03e+02 518 5984 5.04e+02 518 67844 5.05e+02 518 5984 5.06e+02 518 30116 5.07e+02 518 67844 5.08e+02 518 32957 5.09e+02 518 67844 5.10e+02 518 19610 5.11e+02 518 19610 5.12e+02 518 22895 5.13e+02 518 30116 5.14e+02 518 19610 5.15e+02 518 22895 5.16e+02 518 13628 5.17e+02 518 5984 2nd column is the protein atom and the 3rd column the water atom. Chunk of output from an unnamed file without giving the command line that generated it is close to useless :-) Anyway, whatever information is present here is not helping you observe the duration of a contact between the protein and any given water molecule. if iam doing g_dist how is it possible to know the which water molecule has to be considered for the distance calculations ie should i compute the distance between one protein atom against all the water within the cut off individually? If you have read g_dist -h and want to ask this question, then I did not understand your previous statement of your objective. Mark Thanks On Wed, Feb 29, 2012 at 2:12 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au wrote: On 29/02/2012 7:21 PM, aiswarya pawar wrote: Mark, i want to know which water atoms stay within a cut off to protein atom. OK, but as you will read in g_mindist -h, it will count such atoms and not identify which they were... ie i need the duration at which a water resides on the protein atoms. ... and identity of the atoms is needed for measuring duration of contact. g_dist does something like this, and reading g_mindist -h should have prompted you to find this out. Otherwise, you will have to construct an index group for each water molecule, and script a loop to examine each water molecule separately using some tool that observes what you really want to measure. so for that i need the whole 5ns frames because am looking for water molecules which reside more than 50% of time. You also need to be clear about whether you care about continuous contact. Does a water molecule that oscillates at a distance around the cutoff reside about 50% of the time? You still don't need high time resolution for testing whether this analysis might give you the information you want. The water molecules that are in contact for more than 50% of the time (continuous or not) will show up in 5 snapsnots spaced every nanosecond. 5000 snapshots every picosecond is better, but not if you can't afford to wait for it. Mark Thanks On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au 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 mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au 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
[gmx-users] using more processors for g_mindist
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? and will this effect the output in anyways. Thanks, -- Aiswarya B Pawar -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] using more processors for g_mindist
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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] using more processors for g_mindist
Mark, Right now am computing distance between each protein atom against all water atoms, which is taking too long for 5ns run. i cant reduce the frames either the number of water atoms. So is there any alternate. Thanks On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham mark.abra...@anu.edu.auwrote: 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] using more processors for g_mindist
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 mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au 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 gmx-users@gromacs.org mailto:gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. 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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
