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" 0.00000e+00 706 174 132 0 438 1.00000e-01 708 163 140 1 446 2.00000e-01 707 168 137 0 442 3.00000e-01 712 161 136 3 442 4.00000e-01 713 165 134 0 433 5.00000e-01 709 169 133 1 438 6.00000e-01 705 169 137 1 446 7.00000e-01 699 169 142 2 459 8.00000e-01 710 167 133 2 439 9.00000e-01 700 189 122 1 436 1.00000e+00 707 169 136 0 441 1.10000e+00 705 163 144 0 451 1.20000e+00 707 171 133 1 440 1.30000e+00 709 158 145 0 448 1.40000e+00 718 155 138 1 434 1.50000e+00 711 164 137 0 438 1.60000e+00 713 160 139 0 438 1.70000e+00 702 181 129 0 439 1.80000e+00 707 162 142 1 449 1.90000e+00 706 167 139 0 445 2.00000e+00 709 168 135 0 438 2.10000e+00 708 167 136 1 442 2.20000e+00 708 171 133 0 437 2.30000e+00 709 162 140 1 445 2.40000e+00 698 171 142 1 458 2.50000e+00 701 177 133 1 446 2.60000e+00 706 177 129 0 435 2.70000e+00 708 178 126 0 430 2.80000e+00 698 187 127 0 441 2.90000e+00 700 190 120 2 436 3.00000e+00 703 176 131 2 444 3.10000e+00 702 181 127 2 441 3.20000e+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 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