[gmx-users] index file for g_order

[Alan Dodd]

Well, for the terminal methyl, you have no way of
knowing which way the hydrogeons are pointing... So
no.  However, it is worth including the carbonyl
carbon (although it has no hydrogeons, so no order
parameter), as a reference point for the next carbon
down.

--- Arneh Babakhani <ababakha at mccammon.ucsd.edu>
wrote:

> Hi Alan, great, thanks, I suspected something like
> that.
> 
> Then, is there a way to calculate the Scd order
> parameters for these 
> carbons, given that there are no explicit
> hydrogens???
> 
> Arneh
> 
> Alan Dodd wrote:
> > 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 <ababakha at mccammon.ucsd.edu>
> > 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)
> >>
> >> [ababakha at chelinuxtest OrderParameters]$
> >>
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