[gmx-users] index file for g_order
Arneh Babakhani
ababakha at mccammon.ucsd.edu
Mon Jun 5 19:37:15 CEST 2006
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 <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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