Hey You may benefit from the make_ndx command. This allows to make a custom index group and you can add individual atoms as 1 group with only one element.
http://www.gromacs.org/Documentation/Gromacs_Utilities/make_ndx Also, I recommend you decide on a time cut off points using -b (start) -e (end) these will be in frame To decide on which ion you want to use pick a single frame which interests you and use this command: grompp -s .pdb -f .xtc -dump (interest frame).pdb >From there you can see which ion atoms you pymol or coot and then make you >custom index group Cheers, Alex ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of soumadwip ghosh [soumadwipgh...@gmail.com] Sent: Thursday, December 04, 2014 7:25 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] use of g_hbond Hello everyone, I want to calculate the effect of incorporating ions in the grooves and backbones of a double stranded DNA molecule in the hydrogen bonding between the two chains constituting the DNA. I want to calculate the number, distance distribution and the lifetime of H- bonding between base pairs of two chains both in presence and in absence of the sodium ion. As far as I know, from the g_hbond utility of GROMACS we can calculate the hydrogen bond related parameters but I am not quite sure with the indexing. My index group looks like- Group 0 ( System) has 97135 elements Group 1 ( DNA) has 758 elements Group 2 ( NA) has 624 elements Group 3 ( CL) has 602 elements Group 4 ( Water) has 95151 elements Group 5 ( SOL) has 95151 elements Group 6 ( non-Water) has 1984 elements Group 7 ( Ion) has 1226 elements Group 8 ( NA) has 624 elements Group 9 ( CL) has 602 elements Group 10 ( Water_and_ions) has 96377 elements Group 11 ( major) has 376 elements Group 12 ( minor) has 256 elements Group 13 ( chain_A) has 379 elements Group 14 ( chain_B) has 379 elements Group 15 ( chain_A_Na) has 1 elements Group 16 (chain_A_chain_A_Na) has 380 elements Group 17 ( backbone) has 258 elements I decomposed the entire DNA molecule into two segments, chain_A and chain_B so that I can calculate the H-bonding parameters between the two chains. But I dont know what to do when I want to check the H-bonding between chain_A and chain_B in presence of sodium. Should I make a separate group of chainA and Na (say chain_A_Na) and then calculate the h-bonding with chain_B? Am I doing anything wrong? Is it supposed to be done in some other ways? Please help me out with this.Thanks in advance. Regards, Soumadwip Ghosh Senior research fellow, Indian Institute of Technology, Bombay India. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. This email may be confidential and subject to legal privilege, it may not reflect the views of the University of Canterbury, and it is not guaranteed to be virus free. If you are not an intended recipient, please notify the sender immediately and erase all copies of the message and any attachments. Please refer to http://www.canterbury.ac.nz/emaildisclaimer for more information. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.