[gmx-users] System blows up

Guido Leoni guido.leoni at gmail.com
Wed Jan 11 10:35:05 CET 2012

Dear List
I'm newbie to gromacs (sigh). I'm simulating the interaction between two
proteins(chrystallographic structures) following the spider toxin tutorial.
I'm able to correctly minimize ( E<1000) and equilibrate (400 ps ) the
system. No error message appears to me and I'm quite sure that my starting
structures have no steric clashes.
My .mdp files are equal to the tutorial description excepted for the
choosen timesteps (400 ps in equilibration and 1000 ps in dynamics).
When I run the dynamic (launching gromacs with mpi) I retrieve after 7 ps
the following error message
"2 particles communicated to PME node 3 are more than a cell length out of
the domain decomposition cell of their charge group"
I suppose that this is due to the energy of some components that blow up.
Please how can i check which components are responsible for  the problem?
I'm also looking the instruction on the web site but they appear to me a
bit cryptic. For example

If the crash is happening relatively early (within a few steps), set
nstxout (or nstxtcout) to 1, capturing all possible frames.  Watch the
resulting trajectory to see which atoms/residues/molecules become unstable

I looked the resulting trajectories of the 2 proteins with ngmx but they
seem to be always in the box and it is impossible to graphically check the
water molecules .
Many Thanks for any kind of suggestion
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