[gmx-developers] distance restraints and CVS gromacs

[Peter Kasson]

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?