tangxuan82 at gmail.com
Wed Jan 9 21:09:47 CET 2008
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.
>> 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)
>> 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"
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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?
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