<div>Dear List </div><div>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. </div>
<div>My .mdp files are equal to the tutorial description excepted for the choosen timesteps (400 ps in equilibration and 1000 ps in dynamics). </div><div>When I run the dynamic (launching gromacs with mpi) I retrieve after 7 ps the following error message</div>
<div>"2 particles communicated to PME node 3 are more than a cell length out of the domain decomposition cell of their charge group"</div><div>I suppose that this is due to the energy of some components that blow up. </div>
<div>Please how can i check which components are responsible for the problem?</div><div>I'm also looking the instruction on the web site but they appear to me a bit cryptic. For example </div><div><br></div><div>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 first.</div>
<div><br></div><div>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 . </div><div>Many Thanks for any kind of suggestion</div>
<div>Best</div><div><div>Guido</div><div><br></div>
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