[gmx-users] System blows up

Guido Leoni guido.leoni at gmail.com
Fri Jan 13 09:17:05 CET 2012

Dear List and Mark
I followed your suggestions equilibrating the proteins of my complex
separately. In both cases i'm able to correctly equilibrate the system and
to perform a short md of 500ps. So I suppose that when i simulate both
protein together somewhere there is a clash. Now how could I highlight the
problem? In your opinion the clash could be more probably due to solvent
molecules or to my proteins perhaps too near each other?
Thank you very much

2012/1/11 Mark Abraham <Mark.Abraham at anu.edu.au>

> On 11/01/2012 8:35 PM, Guido Leoni wrote:
>> 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
>> first.
>> 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 .
> The next piece of advice is to simplify your problem. If you can get each
> of your proteins to equilibrate on their own, then you probably have an
> atomic clash after all. If one doesn't equilibrate, then maybe your
> simulation conditions or topology is suspect.
> Mark
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Guido Leoni
National Research Institute on Food and Nutrition
via Ardeatina 546
00178 Rome

tel     + 39 06 51 49 41 (operator)
        + 39 06 51 49 4498 (direct)
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