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
er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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