Upgraded it to 3.3.1 now, still get the same error ... Using this command: ############################ g_hbond -f ../76.55-78.95ns.xtc -s ../md_000.tpr -n index.ndx -num hbnum_MGL-MGL ############################ I get this output: ############################ Reading file ../md_000.tpr, VERSION 3.2 (single precision) Note: tpx file_version 31, software version 40 Specify 2 groups to analyze: Group 0 ( DGL) has 158400 elements Group 1 ( MGL) has 100800 elements Group 2 ( DGL_MGL) has 259200 elements Select a group: 1 Selected 1: 'MGL' Select a group: 1 Selected 1: 'MGL' Calculating hydrogen bonds in MGL (100800 atoms) Found 9600 donors and 19200 acceptors Reading frame 0 time 76550.000 Will do grid-seach on 44x46x52 grid, rcut=0.35 ------------------------------------------------------- Program g_hbond, VERSION 3.3.1 Source code file: gmx_hbond.c, line: 669
Range checking error: Variable gx has value -24. It should have been within [ 0 .. 44 ] Please report this to the mailing list ([email protected]) ------------------------------------------------------- ############################ Note, when running the script on the other group in the list, DGL, the error does not occur. However, it takes a very long time under the grid-search process. Not sure whether that should be the case or not with this number of atoms involved or not. I actually left it running for three days and it was still churning away at it with no change to the display. Would it help if in the groups I simply narrowed the index file down to just the atoms that will be involved in the H-bonding? And leave out all the ones the don't? No idea how it handles all the atom lists, so not sure if that will help reduced load or not. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
