[gmx-developers] distance restraints and CVS gromacs

[Berk Hess]

Hi,

I committed a fix and check for the distance restraints.
Full distance restraint support with domain decomposition is not there yet.

There was a fprintf to a NULL pointer, that has been fixed.

Now there is a check for time averaging or multiple pairs per restraint,
in those cases mdrun will give a fatal error with a hint to use particle 
decomposition.
Otherwise it prints a note that the atoms involved in distance 
restraints should
be within the longest cut-off distance.

Berk.

Peter Kasson wrote:
> I'm having a couple sets of errors using distance restraints with CVS 
> Gromacs.
>
> 1.  Parallel execution--I get an immediate segfault when running in 
> parallel.  Relevant portion of output is:
>
> Loaded with Money
>
> [host:09849] *** Process received signal ***
> [host:09849] Signal: Bus error (10)
> [host:09849] Associated errno: Unknown error: 1149974564 (1149974564)
> [host:09849] Signal code:  (1149829269)
> [host:09849] Failing at address: 0x4c894824
> [host:09851] *** Process received signal ***
> [host:09847] *** Process received signal ***
> [host:09847] Signal: Bus error (10)
> [host:09847] Associated errno: Operation not permitted (1)
> [host:09847] Signal code:  (6226608)
> [host:09847] Failing at address: 0x0
> [ 1] [0xbffff158, 0x0000000c] (-P-)
> [ 2] (vfprintf_l + 0x5e) [0xbffff188, 0x900e3b50]
> [ 3] (fprintf + 0x49) [0xbffff1b8, 0x90010c49]
> [ 4] [ 1] [0xbffff158, 0x0000000c] (-P-)
> [ 2] (vfprintf_l + 0x5e) [0xbffff188, 0x900e3b50]
> [ 3] (fprintf + 0x49) [0xbffff1b8, 0x90010c49]
> [ 4] (init_disres + 0x281) [0x0033f740, 0x000fb2bf] (F--)
> [host:09847] *** End of error message ***
> (init_disres + 0x281) [0x0033f740, 0x000fb2bf] (F--)
> [host:09849] *** End of error message ***
>
> 2.  Single-processor execution:  My test run finished successfully, 
> but the box vectors appeared to get set to 0 on the last step of an 
> NVT run.  I am currently trying to reproduce this.  The coordinates 
> still look good, which is odd.
>            Step           Time         Lambda
>            9000        4.50000        0.00000
>
>    Energies (kJ/mol)
>            Bond          Angle Ryckaert-Bell.          LJ-14     
> Coulomb-14
>     4.41356e+04    5.59424e+04    6.98612e+04    2.47973e+04    
> 3.30593e+05
>         LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.     Dis. 
> Rest.
>     1.95581e+05   -1.78487e+04   -2.29260e+06   -2.06173e+05    
> 2.35615e+01
>  D.R.Viol. (nm)      Potential    Kinetic En.   Total Energy    
> Temperature
>     4.76351e-02   -1.79569e+06    4.27210e+05   -1.36848e+06    
> 3.16984e+02
>  Pressure (bar)
>    -3.99388e+01
>
>            Step           Time         Lambda
>           10000        5.00000        0.00000
>
> Writing checkpoint, step 10000 at Sun Jun 29 15:17:53 2008
>
>    Energies (kJ/mol)
>            Bond          Angle Ryckaert-Bell.          LJ-14     
> Coulomb-14
>     4.42875e+04    5.63012e+04    6.97215e+04    2.46440e+04    
> 3.30470e+05
>         LJ (SR)  Disper. corr.   Coulomb (SR)       RF excl.     Dis. 
> Rest.
>     1.93199e+05            nan   -2.29140e+06   -2.06173e+05    
> 2.46423e+01
>  D.R.Viol. (nm)      Potential    Kinetic En.   Total Energy    
> Temperature
>     6.16940e-02            nan    4.28409e+05            nan    
> 3.17873e+02
>  Pressure (bar)
>             nan
>
> Has anyone been using distance restraints successfully with the 
> current CVS version?
>
>
>
>
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