[gmx-users] System blows up

[Guido Leoni]

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
Guido

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
(I.N.R.A.N.)
via Ardeatina 546
00178 Rome
Italy

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