[gmx-users] single and parallel

[Dmitry Kovalsky]

Dear users,

I'm trying to setup gromacs on pararllel and have encounterd a problem. 
When a perpared system protein_water_ions is subjected to postion restraint 
dynamics using mdrun_mpi I always got 

    Step           Time         Lambda      Annealing
            500        0.25000        0.00000        1.00000

   Energies (kJ/mol)
        G96Bond       G96Angle    Proper Dih.  Improper Dih.          LJ-14
    2.43359e+05    8.83435e+04    6.04327e+03    1.91688e+04    6.71810e+03
     Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)
    9.06309e+03    1.43625e+05   -2.14673e+03   -3.91914e+05   -2.07263e+02
 Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
    2.11158e+06    2.23363e+06    7.87225e+05    3.02086e+06    3.81554e+03
 Pressure (bar)
    5.50371e+04

Large VCM(group rest):     44.17586,      0.10379,    -11.13218, ekin-cm: 
160105760.00000

t = 0.298 ps: Water molecule starting at atom 3907 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
previous and current coordinates
           Step           Time         Lambda      Annealing
            600        0.30000        0.00000        1.00000
        Step           Time         Lambda      Annealing
           1000        0.50000        0.00000        1.00000

xx[    0] before: (     nan,     nan,     nan) After: (     nan,     nan,   
nan)
xx[    1] before: (     nan,     nan,     nan) After: (     nan,     nan,     
nan)
xx[    2] before: (     nan,     nan,     nan) After: (     nan,     nan,     
nan)
xx[    3] before: (     nan,     nan,     nan) After: (     nan,     nan,     
nan)
xx[    4] before: (     nan,     nan,     nan) After: (     nan,     nan,     
nan)
xx[    5] before: (     nan,     nan,     nan) After: (     nan,     nan,     
nan)
xx[    6] before: (     nan,     nan,     nan) After: (     nan,     nan,     
nan)

In case when I'm doing the same  at  single processor I donn't get any 
warnings
and it finishes correctly
Where is the difference ?
-- 
Sincerely yours,

Dima

Ph.D. Student Dmitry Kovalsky
Institute of Molecular Biology & Genetics
150 Akad. Zabolotnogo Street,
Kiev-143, 03143
UKRAINE

E-mail: dikov at imbg.org.ua
Fax:  +380 (44) 266-0759
Tel.: +380 (44) 266-5589