[gmx-users] xtc, rmsd

[David van der Spoel]

Michal Kolinski wrote:
> Hi all
> I'm trying to calculate the rmsd for C-alpha in my system (for 2ns long MD).
> When I:
>  
> g_rms_gmx33 -s po -n grupy.ndx -f po -o rmsd_mu
>  
>  
> I get the following error:
>  
> ...
> ....
> .......
>  
> Group    10 ( Prot-Masses) has  4009 elements
> Group    11 ( Non-Protein) has 31709 elements
> Group    12 (        DPPC) has  5200 elements
> Group    13 (         SOL) has 26478 elements
> Group    14 (          Cl) has     7 elements
> Group    15 (       Other) has 31709 elements
> Group    16 (      MU_FIX) has   695 elements
> Select a group: 16
> Selected 16: 'MU_FIX'
> Reading frame     390 time  780.000   
> -------------------------------------------------------
> Program g_rms_gmx3, VERSION 3.3
> Source code file: xtcio.c, line: 83
>  
> Fatal error:
> Magic Number Error in XTC file (read 0, should be 1995)
> -------------------------------------------------------
>  
> "Step Aside, Butch" (Pulp Fiction
>  
>  
>  
> Please give me some suggestions what might be  the problem, and how to 
> fix it?
> (I’m using GROMACS_3.3)

probably a broken xtc file or the 2 Gb limit on an old OS.

run gmxcheck on it.


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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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