Mark, In the g_mindist output data gives which atom was within cutoff to protein atom ie the output file of g_mindist
5.000000e+02 518 42680 5.010000e+02 518 20942 5.020000e+02 518 67844 5.030000e+02 518 5984 5.040000e+02 518 67844 5.050000e+02 518 5984 5.060000e+02 518 30116 5.070000e+02 518 67844 5.080000e+02 518 32957 5.090000e+02 518 67844 5.100000e+02 518 19610 5.110000e+02 518 19610 5.120000e+02 518 22895 5.130000e+02 518 30116 5.140000e+02 518 19610 5.150000e+02 518 22895 5.160000e+02 518 13628 5.170000e+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.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>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>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 >>> 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 list 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. >> 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 > 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
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