[gmx-users] single and parallel

[David]

On Thu, 2002-07-18 at 10:35, Dmitry Kovalsky wrote:
> 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
Look here ^^^^^^

The whole energy is determined by position restraints. That means you
are restraining with the wrong coordinates as reference positions

>  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
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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