Sir, >From Index file which gives the unique contacts - First section the list of atoms I want to analyse [ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]
second section : the unique contacts of each atoms with others [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ] 5 7ws 5 10 5 14 5 18 5 22 5 24 5 27 5 30 5 35 5 292 5 296 5 30 >From this second section Total contacts was extracted for each atom and compared with that from a second simulation. These contacts was matching with the contacts of the 3rd column from g_mdmat output - @ legend string 0 "Total/mean" @ legend string 1 "Total" @ legend string 2 "Mean" @ legend string 3 "# atoms" @ legend string 4 "Mean/# atoms" #res ratio tot mean natm mean/atm 1 1.001 11 10.991 1 10.991 2 1.244 10 8.041 1 8.041 3 1.166 13 11.147 1 11.147 4 1.036 11 10.615 1 10.615 While the time dependent contacts in the xvg file shows that the first simulation has more contacts than the second one.. I hope I am clear this time. Thank you kavya On Mon, Mar 4, 2013 at 10:05 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 3/4/13 11:25 AM, Kavyashree M wrote: > >> Dear users, >> >> I used the following tool for finding the contacts >> g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn >> a.ndx >> -num a.xvg >> >>> From the index file, the number of contacts of each atom was extracted. >>> >> This and the >> xvg output was compared with another simulation. >> It was found that the number of contacts was more in 2nd simulation >> compared to >> the first. But When I compared xvg file it was showing the opposite >> behaviour. >> > > These statements don't make any sense. How did you determine that the > number of contacts in simulation 2 was greater than simulation 1, but then > the .xvg files showed the opposite? The number of contacts come from the > .xvg files? Perhaps you simply swapped your files during analysis. > > > The contacts was also calculated using g_mdmat for the same cutoff and it >> was agreeing >> with the numbers I got from in index output of g_hbond. >> >> Why is this difference in index and xvg output? >> > > An index group is a list of atom numbers. The .xvg output is whatever you > tell it to be, in this case, the number of contacts within the group > selected. > > -Justin > > > Also the xvg file looks like - >> >> s0 legend "Contacts" >> @ s1 legend "Pairs within 0.4 nm" >> 4000 7496 0 >> 4002 7513 0 >> 4004 7605 0 >> 4006 7531 0 >> 4008 7573 0 >> 4010 7546 0 >> 4012 7544 0 >> 4014 7526 0 >> 4016 7530 0 >> 4018 7496 0 >> 4020 7526 0 >> .. >> >> >> Thank you >> kavya >> >> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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