[gmx-users] Anybody please explain this log message?

[David van der Spoel]

On Wed, 2002-08-14 at 10:49, Vishal Vaidyanathan wrote:
> Hi,
>   Attached below is a snippet of md.log when I run a  simulation with
> increased time step, dummy hydrogens and without pbc.
> 
>   nstcomm was set to -1 to remove rotational motion and the integrator
> used is sd. Setting/unsetting T and/or P coupling does not seem to have
> any effect on this.
> 
>   I don't get any LINCS warning or errors and the trajectory seems
> reasonable on visualisation.
> 
>   Does anyone know what these messages mean? Is the trajectory valid?
If this is at the first step, then it is just the initial velocities
being corrected. Otherwise something weird has happened. Check you
energies at this timestep.

> 
>   Thanks a lot,
> 							Vishal
> 
> =====================================================================
> 
> 
> Large VCM(group rest):      0.01488,     -0.02237,      0.03087, ekin-cm:
> 1
> .59499
> Group rest with mass   1905.01172, Ekrot      1.09969 Det(I) =
> 15735759.83967
>   COM:     -0.73445      -1.49617       2.30917
>   P:       -0.60753      -8.48648      35.31365
>   V:       -0.00032      -0.00445       0.01854
>   J:       -3.65605     -21.78838     -20.26941
>   w:       -0.01412      -0.04088      -0.06202
> Inertia tensor (3x3):
>    Inertia tensor[    0]={ 2.34860e+02,  4.84612e+01,  5.69241e+01}
>    Inertia tensor[    1]={ 4.84612e+01,  1.74373e+02,  1.05347e+02}
>    Inertia tensor[    2]={ 5.69241e+01,  1.05347e+02,  4.74710e+02}
> 
> =====================================================================
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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