Dear gmx-users,
I have done simulations of one small molecule that diffuses into a DMPC membrane. This small molecule contains an alcohol group and is therefore capable of hydrogen bonding to the oxygens of DMPC (phosphate and glycerol region). I have read the manual (section 8.12 and g_hbond -h), searched the mailing list and google but I have not been able to find a more thorough description of the output possibilities than in the manual. I have tried three different approaches: 1. The -OH group of the small molecule and the glycerol oxygens 2. The -OH group of the small molecule and the phosphate oxygens 3. The small molecule and DMPC (no subgroups) No. 1 gives 38 hbond, no. 2 gives 15 hbonds and no. 3 gives 53 hbonds. So 1 + 2 = 3, which is fine. Below is the output from no. 1: (gromacs 4.0.4) Specify 2 groups to analyze: Selected 0: 'O11_&_PALC_H12_&_PALC' Selected 1: 'O7_&_DMPC_&_DMPC_O9_&_DMPC_O10_&_DMPC' Checking for overlap in atoms between O11_&_PALC_H12_&_PALC and O7_&_DMPC_&_DMPC_O9_&_DMPC_O10_&_DMPC Calculating hydrogen bonds between O11_&_PALC_H12_&_PALC (2 atoms) and O7_&_DMPC_&_DMPC_O9_&_DMPC_O10_&_DMPC (384 atoms) Found 1 donors and 385 acceptors Making hbmap structure...done. Will do grid-seach on 15x15x24 grid, rcut=0.35 Found 15 different hydrogen bonds in trajectory Found 23 different atom-pairs within hydrogen bonding distance Merging hbonds with Acceptor and Donor swapped - Reduced number of hbonds from 15 to 15 - Reduced number of distances from 23 to 23 Average number of hbonds per timeframe 0.083 out of 192.5 possible What does these "15 different hydrogen bond in trajectory" mean? I don't understand this. I also don't understand "Average number of hbonds per timeframe 0.083 out of 192.5 possible" - 192.5 possible hbonds?? Can anyone shed some light on this? Another question relates to the lifetime of the hbond calculated when the "-life" flag is given. The produced .xvg file contain three columns: time, p(t), and t p(t). What is p(t) and t p(t)? And how can I find the lifetime? Thank you in advance, Sarah -- 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/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/mailing_lists/users.php
