Ok great, will do, thanks for your help!
Alan Dodd wrote:
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 <[EMAIL PROTECTED]>
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 <[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]$
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