[gmx-users] g_covar

[tangxuan]

Berk Hess wrote:
> This is an incorrect warning, which has been introduced in
> version 3.3.2. I have corrected the warning for 3.3.3.
>
> Berk.
>
>   
>> Date: Wed, 9 Jan 2008 14:51:52 +0100
>> From: tangxuan82 at gmail.com
>> To: gmx-users at gromacs.org
>> Subject: [gmx-users] g_covar
>>
>> Dear all,
>> When I am using g_covar to calculate the covariance matrix for alpha 
>> carbons in one subunit of my protein, I get a warning" WARNING number of 
>> atoms in tpx (929) and trajectory (293401) do not match". 929 is the 
>> alpha carbon number and 293401 is  whole system atom number. In the 
>> command, I used trr file and tpr file of the whole system. Do I have to 
>> get a new trr file and tpr file just for these alpha carbons? 
>> Some information  is shown below.
>> "Group     0 (      System) has 293401 elements
>> Group     1 (     Protein) has 75295 elements
>> Group     2 (   Protein-H) has 38096 elements
>> Group     3 (     C-alpha) has  4831 elements
>> Group     4 (    Backbone) has 14493 elements
>> Group     5 (   MainChain) has 19340 elements
>> Group     6 (MainChain+Cb) has 23750 elements
>> Group     7 ( MainChain+H) has 23963 elements
>> Group     8 (   SideChain) has 51332 elements
>> Group     9 ( SideChain-H) has 18756 elements
>> Group    10 ( Prot-Masses) has 75295 elements
>> Group    11 ( Non-Protein) has 218106 elements
>> Group    12 (         KCX) has   184 elements
>> .
>> .
>> Group   107 (chO_chV_&_C-alpha) has   929 elements
>> Select a group: 107
>> Selected 107: 'chO_chV_&_C-alpha'
>> Calculating the average structure ...
>> trn version: GMX_trn_file (single precision)
>> Reading frame       0 time 20000.000  
>> WARNING number of atoms in tpx (929) and trajectory (293401) do not match
>> Last frame       1000 time 30000.000  
>>
>> Last frame       1000 time 30000.000   to ./#average.pdb.17#
>> Read 1001 frames
>>
>> Trace of the covariance matrix: 2.34563 (nm^2)
>> 100%
>> Diagonalizing ...
>>
>> Sum of the eigenvalues: 2.34563 (nm^2)
>>
>> Writing eigenvalues to eigenval.xvg
>>
>> Writing reference, average structure & eigenvectors 1--1000 to eigenvec.trr
>> Wrote the log to covar.log"
>>
>> Tang
>>
>>
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>
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>   
Thanks for your reply. I have another question. I can get the 
coordinates covariance by option -ascii, but do you know how to get a 
exact covariance value for each atom?

Thanks

Tang