[gmx-users] what error!

[David van der Spoel]

chiloo Laohpongspaisan wrote:
> Dear all,
>  
> i have got the abnormal values of torsion angle by using g_angle of gromacs.
>  
> g_angle -f whole.xtc -s md.tpr -n index.ndx -ov out_avrg.xvg -od 
> out_dist.xvg -type dihedral
>  
> i use such tool in many systems, the torsions along time seem to be 
> normal except one. And the values are as below.
>  0.00000   114.224
>    0.50000   148.269
>    1.00000   111.814
>    1.50000   134.277
>    2.00000   119.016
>    2.50000   164.146
>    3.00000   135.531
>    3.50000   155.514
>    4.00000   141.842
>    4.50000   119.932
>    5.00000   167.298
>    5.50000   142.312
>    6.00000   137.572
>    6.50000   120.933
>    7.00000   102.041
>    7.50000   110.602
>    8.00000   115.885
>    8.50000   121.182
>    9.00000   129.657
>    9.50000   139.459
>   10.00000   103.588
> .
> .
> .
> 2176.50000   619.006
> 2177.00000   578.398
> 2177.50000   604.184
> 2178.00000   613.300
> 2178.50000   616.644
> 2179.00000   624.160
> 2179.50000   589.085
> 2180.00000   623.641
> 2180.50000   587.703
> 2181.00000   602.743
> 2181.50000   609.376
> 2182.00000   615.177
> 2182.50000   589.517
> 2183.00000   600.030
> 2183.50000   597.635
> 2184.00000   611.222
> 2184.50000   565.024
> 2185.00000   623.541
> .
> .
> .
> 7995.50049  -590.026
> 7996.00049  -548.768
> 7996.50049  -574.251
> 7997.00049  -530.451
> 7997.50049  -591.581
> 7998.00049  -571.748
> 7998.50049  -541.372
> 7999.00049  -528.471
> 7999.50049  -559.895
> 8000.00049  -602.409
> 
>  
> Anyone knows my problem, suggest me please.
>  

try the -periodic flag
(3.3.1 only IIRC)


> Best regards,
> Chiloo
> 
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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://folding.bmc.uu.se
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