The first and last carbons are not calculated. GROMACS needs to use a C-C bond on either side of each carbon to place the hydrogens, and hence calculate the order parameter.
--- Arneh Babakhani <[EMAIL PROTECTED]> wrote: > Hello, > > Now with the g_order bug fixed (see bugzilla #84) , > I'm trying to > calculate the orderparameters for 13 carbon atoms of > the the sn2 chain > (carbons 2B thru 2N) of a DMPC membrane. So I > create an index file, > make a group for each type of carbon, then run > g_order. > > The groups in the index file are recognized (as can > be seen below, where > I've pasted an excerpt from my terminal). All 13 > carbon groups are there. > > But the output is a list of order parameters for > only 11 carbons (I > think the last two groups, C2M and C2N, are > truncated off). Is this > right? If so, how do I calculate the order > parameters for C2M and C2N ? > Or, is this another bug? > > Thanks, > > Arneh > > ----------------------------------- > Taking z axis as normal to the membrane > Reading file ../FullMD1.tpr, VERSION 3.1.4 (single > precision) > Note: tpx file_version 24, software version 40 > Note: nLincsIter not in run input file, setting it > to 1 > Using following groups: > Groupname: C2B First atomname: C2B First atomnr 16 > Groupname: C2C First atomname: C2C First atomnr 17 > Groupname: C2D First atomname: C2D First atomnr 18 > Groupname: C2E First atomname: C2E First atomnr 19 > Groupname: C2F First atomname: C2F First atomnr 20 > Groupname: C2G First atomname: C2G First atomnr 21 > Groupname: C2H First atomname: C2H First atomnr 22 > Groupname: C2I First atomname: C2I First atomnr 23 > Groupname: C2J First atomname: C2J First atomnr 24 > Groupname: C2K First atomname: C2K First atomnr 25 > Groupname: C2L First atomname: C2L First atomnr 26 > Groupname: C2M First atomname: C2M First atomnr 27 > Groupname: C2N First atomname: C2N First atomnr 28 > > trn version: GMX_trn_file (single precision) > Reading frame 0 time 0.000 Number of > elements in first group: 128 > Last frame 150 time 150.000 > > Read trajectory. Printing parameters to file > Atom 1 Tensor: x=-0.225996 , y=-0.226754, z=0.452751 > Atom 2 Tensor: x=-0.22165 , y=-0.246523, z=0.468173 > Atom 3 Tensor: x=-0.229328 , y=-0.215539, z=0.444867 > Atom 4 Tensor: x=-0.230127 , y=-0.199614, z=0.429741 > Atom 5 Tensor: x=-0.24599 , y=-0.185492, z=0.431482 > Atom 6 Tensor: x=-0.221037 , y=-0.179952, z=0.400989 > Atom 7 Tensor: x=-0.226934 , y=-0.170633, z=0.397566 > Atom 8 Tensor: x=-0.203112 , y=-0.165726, z=0.368838 > Atom 9 Tensor: x=-0.191929 , y=-0.145227, z=0.337156 > Atom 10 Tensor: x=-0.164109 , y=-0.118401, z=0.28251 > Atom 11 Tensor: x=-0.154092 , y=-0.0753129, > z=0.229405 > > Back Off! I just backed up order.xvg to > ./#order.xvg.11# > > Back Off! I just backed up deuter.xvg to > ./#deuter.xvg.7# > > gcq#146: "We All Get the Flu, We All Get Aids" > (LIVE) > > [EMAIL PROTECTED] OrderParameters]$ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
