On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul <jalem...@vt.edu> wrote:
> > When measuring contacts, you don't measure one group, you measure the > number of contacts that occur between groups A and B, which considers all > atoms in those two groups. > I gave a group of hydrophobic atoms in both cases The command I gave - g_hbond_46 -f x.xtc -s x.tpr -contact -n x.ndx -r 0.4 -hbm o.xpm -hbn o.ndx -num o.xvg my index file contained a group of hydrophobic atoms. which I supplied in the x.ndx. > > You don't define contacts in an index group, you define atoms that may or > may not make contacts with others. > > The one I mentioned here is the output index file from the g_hbond (4.6 version) - o.ndx. > > [ 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 >> >> > There's something very wrong with this index file. How did you generate > it? The presence of a repeated atom number (5) and a nonsensical one (7ws) > leads me to believe that you've done something incorrect. Did this come > from g_hbond? It looks like the output of -hbn, which is only useful for > decoding hbmap.xpm, nothing else. > > I did not generate this. The tool (g_hbond) generated this index file. It is the -hbn output. > > 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.. >> >> > That shouldn't be unexpected. Two independent simulations have no > guarantee of doing the same thing, that's why sampling is so important. > Thank you kavya -- 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