[gmx-users] stopping mdrun without error massage

[Carsten Kutzner]

Dear Karim,

a (small) load imbalance is perfectly normal for a parallel
simulation and no need to switch over to particle decomposition
(both domain and particle decomposition should however work).
Are you shure you get no error message? People will need some
more information here to be able to help. It is  usually
a good idea to include which MPI lib you are using
and the exact command line how you invoked mdrun. You could
anyway try to run on a single processor only and see whether
this scenario also "stops" or whether you get a proper
error message or core file.

Carsten


On Dec 22, 2010, at 12:34 PM, Mahnam wrote:

> In God We Trust 
> Hello Dear GMX users 
> I want to do MD on one peptide in water with gromacs 4.5.3. 
> I minimized and equilibrated my system in NPT and NVT for 50 ps , but when I do final mdrun it has load imbalance and when I try  -pd option it stops after 265 ps without any error massage !, can everybody help me. 
> Here is my mdp file .
> constraints         =  hbonds 
> integrator          =  md 
> dt                  =  0.002 
> nsteps              =  50000000 
> nstcomm             =  10 
> comm_mode           =  Linear 
> comm_grps           =  protein 
> nstxout             =  250 
> nstvout             =  1000 
> nstfout             =  0 
> nstcalcenergy       =  10 
> nstlog              =  1000 
> nstenergy           =  1000 
> nstlist             =  10 
> ns_type             =  grid 
> rlist               =  1.2 
> coulombtype         =  PME 
> rcoulomb            =  1.2 
> rvdw                =  1.4 
> fourierspacing      =  0.12 
> fourier_nx          =  0 
> fourier_ny          =  0 
> fourier_nz          =  0 
> pme_order           =  4 
> ewald_rtol          =  1e-5 
> optimize_fft        =  yes 
> energygrps          = protein  SOL 
>      
>   
> ; Berendsen temperature coupling is on in three groups 
> Tcoupl              =  v-rescale 
> tau_t               =  0.1       1      
> tc-grps      =  protein   bulk    
> ref_t               =  300       300        
> ; Pressure coupling is  on 
> Pcoupl              =  parrinello-Rahman 
> tau_p               =  1 
> compressibility     =  4.5e-5 
> ref_p               =  1.0 
> ; Generate velocites is on at 300 K. 
> gen_vel             =  yes 
> gen_temp            =  300.0 
> gen_seed            =  173529
>  
> 
> Many thanks in advance for your help and your reply. 
> Yours truly 
> Karim Mahnam 
> Institute of  Biochemistry  and  Biophysics (IBB) 
> Tehran University 
> P.O.box 13145-1384 
> Tehran 
> Iran 
> http://www.ibb.ut.ac.ir/ 
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne