Re: [gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1
Hi All: Has there been further resolution on the difference between g_hbond in v 4.0 and 4.5 (I'm running 4.5.3)? For counting water-water (tip4p) h-bonds in a box of 506 waters I get the following nhbdist output, which appears to neglect pbc since there are such a large number of unbound donor-H (and the other columns are consequently too low): @title Number of donor-H with N HBs @xaxis label Time (ps) @yaxis label N @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend 0 HBs @ s1 legend 1 HB @ s2 legend 2 HBs @ s3 legend 3 HBs @ s4 legend Total 0.0e+00 706 174 132 0 438 1.0e-01 708 163 140 1 446 2.0e-01 707 168 137 0 442 3.0e-01 712 161 136 3 442 4.0e-01 713 165 134 0 433 5.0e-01 709 169 133 1 438 6.0e-01 705 169 137 1 446 7.0e-01 699 169 142 2 459 8.0e-01 710 167 133 2 439 9.0e-01 700 189 122 1 436 1.0e+00 707 169 136 0 441 1.1e+00 705 163 144 0 451 1.2e+00 707 171 133 1 440 1.3e+00 709 158 145 0 448 1.4e+00 718 155 138 1 434 1.5e+00 711 164 137 0 438 1.6e+00 713 160 139 0 438 1.7e+00 702 181 129 0 439 1.8e+00 707 162 142 1 449 1.9e+00 706 167 139 0 445 2.0e+00 709 168 135 0 438 2.1e+00 708 167 136 1 442 2.2e+00 708 171 133 0 437 2.3e+00 709 162 140 1 445 2.4e+00 698 171 142 1 458 2.5e+00 701 177 133 1 446 2.6e+00 706 177 129 0 435 2.7e+00 708 178 126 0 430 2.8e+00 698 187 127 0 441 2.9e+00 700 190 120 2 436 3.0e+00 703 176 131 2 444 3.1e+00 702 181 127 2 441 3.2e+00 694 184 134 0 452 I've tried playing with different index assignments, and I get what appears to be a reasonable output for 0 HBs by making the two groups appear different, excluding the dummy atom from one. Although, because the program then double counts, the other columns don't convey the intended information. Robin -- Robin C. Underwood Chemistry Department 560 Oval Drive West Lafayette, IN 47907 -- 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] g_hbond results inconsistent between v4.0.7 and v4.5.1
Hi, No. But I hope to get it done this week. Thanks for the reminder. Erik Robin C. Underwood skrev 2010-12-05 19.19: Hi All: Has there been further resolution on the difference between g_hbond in v 4.0 and 4.5 (I'm running 4.5.3)? For counting water-water (tip4p) h-bonds in a box of 506 waters I get the following nhbdist output, which appears to neglect pbc since there are such a large number of unbound donor-H (and the other columns are consequently too low): @title Number of donor-H with N HBs @xaxis label Time (ps) @yaxis label N @TYPE xy @ view 0.15, 0.15, 0.75, 0.85 @ legend on @ legend box on @ legend loctype view @ legend 0.78, 0.8 @ legend length 2 @ s0 legend 0 HBs @ s1 legend 1 HB @ s2 legend 2 HBs @ s3 legend 3 HBs @ s4 legend Total 0.0e+00 706 174 132 0 438 1.0e-01 708 163 140 1 446 2.0e-01 707 168 137 0 442 3.0e-01 712 161 136 3 442 4.0e-01 713 165 134 0 433 5.0e-01 709 169 133 1 438 6.0e-01 705 169 137 1 446 7.0e-01 699 169 142 2 459 8.0e-01 710 167 133 2 439 9.0e-01 700 189 122 1 436 1.0e+00 707 169 136 0 441 1.1e+00 705 163 144 0 451 1.2e+00 707 171 133 1 440 1.3e+00 709 158 145 0 448 1.4e+00 718 155 138 1 434 1.5e+00 711 164 137 0 438 1.6e+00 713 160 139 0 438 1.7e+00 702 181 129 0 439 1.8e+00 707 162 142 1 449 1.9e+00 706 167 139 0 445 2.0e+00 709 168 135 0 438 2.1e+00 708 167 136 1 442 2.2e+00 708 171 133 0 437 2.3e+00 709 162 140 1 445 2.4e+00 698 171 142 1 458 2.5e+00 701 177 133 1 446 2.6e+00 706 177 129 0 435 2.7e+00 708 178 126 0 430 2.8e+00 698 187 127 0 441 2.9e+00 700 190 120 2 436 3.0e+00 703 176 131 2 444 3.1e+00 702 181 127 2 441 3.2e+00 694 184 134 0 452 I've tried playing with different index assignments, and I get what appears to be a reasonable output for 0 HBs by making the two groups appear different, excluding the dummy atom from one. Although, because the program then double counts, the other columns don't convey the intended information. Robin -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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
[gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1
Has anybody checked g_hbond results for consistency between v4.0.7 and v4.5.1? My usage is: g_hbond -f my.xtc -r 0.68 -contact -life -s my.tpr -ac and I find that the output files hbnum.xvg, hbac.xvg, hblife.xvg, and the ac-reported lifetime of interactions are all different. To show the simplest metric, here are the differences for hbnum.xvg: paste hbnum.4.0.7.xvg hbnum.4.5.1.xvg|grep -v '[#|@]'|head 0 135 0 0 97 0 50 143 0 50 101 0 100 135 0 100 95 0 150 143 0 150 100 0 200 142 0 200 100 0 250 133 0 250 96 0 300 143 0 300 100 0 350 135 0 350 91 0 400 144 0 400 97 0 450 140 0 450 95 0 If I redo this, selecting only a single acceptor atom and 64 donor atoms, with a large cutoff distance of 3 nm, v4.0.7 gives me 44 contacts in one frame while v4.5.1 gives me only 1 contact. g_dist confirms that there are 44 contacts within 4 nm (using both versions of g_dist). Then I looked at the more standard actual h-bond usage for a single frame and gave SOL SOL as the selection. The numbers of h-bonds vary widely: 3915 vs. 7836. These numbers are nearly separated by 2x, but not exactly 2x. I can find no record of any intentional changes. gpc-f109n001-$ echo -e SOL\nSOL\n | /project/pomes/cneale/GPC/exe/intel/gromacs-4.0.5/exec/bin/g_hbond -f ../../8ns/RESULTS/3.2/0/0/0-205ns.xtc -n index.ndx -s make_nrexl10_tpr/nrexl10.gromacs4.0.5.tpr -e 0 :-) G R O M A C S (-: Gromacs Runs One Microsecond At Cannonball Speeds :-) VERSION 4.0.5 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) /project/pomes/cneale/GPC/exe/intel/gromacs-4.0.5/exec/bin/g_hbond (-: Option Filename Type Description -f ../../8ns/RESULTS/3.2/0/0/0-205ns.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt -s make_nrexl10_tpr/nrexl10.gromacs4.0.5.tpr InputRun input file: tpr tpb tpa -n index.ndx Input, Opt! Index file -num hbnum.xvg Output xvgr/xmgr file -g hbond.log Output, Opt. Log file -ac hbac.xvg Output, Opt. xvgr/xmgr file -disthbdist.xvg Output, Opt. xvgr/xmgr file -ang hbang.xvg Output, Opt. xvgr/xmgr file -hxhbhelix.xvg Output, Opt. xvgr/xmgr file -hbn hbond.ndx Output, Opt. Index file -hbm hbmap.xpm Output, Opt. X PixMap compatible matrix file -don donor.xvg Output, Opt. xvgr/xmgr file -dan danum.xvg Output, Opt. xvgr/xmgr file -lifehblife.xvg Output, Opt. xvgr/xmgr file -nhbdistnhbdist.xvg Output, Opt. xvgr/xmgr file Option Type Value Description -- -[no]h bool no Print help info and quit -niceint19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]xvgrbool yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program -[no]ins bool no Analyze solvent insertion -a real 30 Cutoff angle (degrees, Acceptor - Donor - Hydrogen) -r real 0.35Cutoff radius (nm, X - Acceptor, see next option) -[no]da bool yes Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE) -r2 real 0 Second cutoff radius. Mainly useful with -contact and -ac -abinreal 1 Binwidth angle distribution (degrees) -rbinreal 0.005 Binwidth distance distribution (nm) -[no]nitacc bool yes Regard nitrogen atoms as acceptors
[gmx-users] g_hbond results inconsistent between v4.0.7 and v4.5.1
If I redo this, selecting only a single acceptor atom and 64 donor atoms, with a large cutoff distance of 3 nm, v4.0.7 gives me 44 should have read 4 nm above. the point is that there really are 44 contacts, but v4.5.1 reports only 1. contacts in one frame while v4.5.1 gives me only 1 contact. g_dist confirms that there are 44 contacts within 4 nm (using both versions of g_dist). -- 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] g_hbond results inconsistent between v4.0.7 and v4.5.1
chris.ne...@utoronto.ca skrev 2010-10-15 16.58: If I redo this, selecting only a single acceptor atom and 64 donor atoms, with a large cutoff distance of 3 nm, v4.0.7 gives me 44 should have read 4 nm above. the point is that there really are 44 contacts, but v4.5.1 reports only 1. contacts in one frame while v4.5.1 gives me only 1 contact. g_dist confirms that there are 44 contacts within 4 nm (using both versions of g_dist). I recall streamlining some pbc-related things. Perhaps I need to revisit that part of the code. -- --- Erik Marklund, PhD student Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:+46 18 471 4537fax: +46 18 511 755 er...@xray.bmc.uu.sehttp://folding.bmc.uu.se/ -- 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
