[gmx-users] problems with some calculated trajectories

[Bernhard Knapp]

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
[...]