[gmx-users] problems with some calculated trajectories

[Erik Marklund]

Hi,

Could it be a periodicity issue? Have you tried using trjconv -pbc nojump ?

/Erik

Bernhard Knapp skrev:
> Dear users
>
> I performed some long-time simulations using gromacs 4.0. The longest 
> simulation trajectory is about 62 ns. Unfortunately the trajectory 
> seems to be damaged. If I calculate the RMSD of different interesting 
> regions the values are beginning to jump up an down after about 17 ns 
> in one case an after about 51ns in another case. At 17802 the RMSD is 
> at 0.23 nm and at the next step (3ps later) the RMSD is at 5.14 nm at 
> 17826 it is normal again (see below). This usually happens only late 
> in the simulation - in a second trajectory this occurs first at about 
> 51 ns. Is it possible that the integration step with 3fs is too big? 
> In other systems it worked fine (also parameterized with the 3 
> integration step) but there I always stopped the calculation after 
> about 25 ns. Unfortunately I can not visualize these steps in VMD 
> because it simply crashing without giving a reason when trying to load 
> on of the "jumping" trajectories.
> Any ideas where the problem is? Gromacs itself never crashed. Are 
> those trajectories lost (a lot of cpu-time was used to calculate them)?
>
> cheers
> Bernhard
>
>
> # This file was created Mon Jun 22 15:37:12 2009
> # by the following command:
> # g_rms -f testSystem.md.trr -s testSystem.md.tpr -o 
> rmsd.TcrCdrs.fitpMHC.xvg -n index.cdrsAndStrands.ndx -ng 6
> [...]
> @ s0 legend "r_208-220"
> @ s1 legend "r_233-244"
> @ s2 legend "r_276-289"
> @ s3 legend "r_320-332"
> @ s4 legend "r_344-357"
> @ s5 legend "r_389-402"
> [...]
> 17799.0000000    0.2338723    0.3308447    0.2894795    0.3391822    
> 0.3839697    0.3377238
> 17802.0000000    0.2085721    0.3414616    0.2959754    0.3393066    
> 0.3958026    0.3484098
> 17805.0000000    5.1469097    6.1970301    5.1444921    4.8545394    
> 4.3217993    5.2186780
> 17808.0000000    5.1355081    6.1895332    5.1366892    4.8242044    
> 4.3055258    5.1988029
> 17811.0000000    5.1066484    6.1653795    5.1244779    4.8204927    
> 4.3008566    5.2036052
> 17814.0000000    5.1628337    6.1792722    5.1491256    4.8215613    
> 4.2966776    5.2330446
> 17817.0000000    5.1292739    6.1900868    5.1392283    4.8198600    
> 4.3028598    5.2275128
> 17820.0000000    5.1841335    6.2482085    5.1694412    4.8562689    
> 4.3307199    5.2453709
> 17823.0000000    5.1587186    6.2190604    5.1589088    4.8293381    
> 4.3215928    5.2137132
> 17826.0000000    0.2097420    0.3379748    0.2840363    0.3228907    
> 0.3922718    0.3273460
> [...]
>
>
>
>
>
>
>
>
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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys