[gmx-users] question in pulling in gromacs 4.0

[Mark Abraham]

anirban polley wrote:
> Hi ,
>       I want to pull a molecule from the membrane. My complete mdp file 
<snip>
> ; GENERATE VELOCITIES FOR STARTUP RUN =
> gen_vel                  = yes
> gen_temp                 = 310.0
> gen_seed                 = 173529

Equilibrate first, then do funky things.

> Here, in the first step, there is no error or warning during the making 
> of .tpr file.    But in the mdrun, after 3/4 steps, it crashes ans stop 
> the MD run. It gives the following error message:
>            Back Off! I just backed up dppc_pip2-ion_NPT_berendsen_md.edr 
> to ./#dppc_pip2-ion_NPT_berendsen_md.edr.2#
> starting mdrun 'Pure 122 DPPC and 1 PIP2 molecule bilayer with 3592 
> water molecules'
> 1750000 steps,   3500.0 ps.
> step 0
> 
> Step 1  Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511
> 
> Step 1  Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511
> 
> Step 1  Warning: pressure scaling more than 1%, mu: 1.00054 1.00054 0.83511
> .............................................
> 
> t = 500.004 ps: Water molecule starting at atom 10595 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> 
> Step 2, time 500.004 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> rms 35.655980, max 638.714233 (between atoms 2849 and 2848)
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint length
>     943    942   54.9    0.1498   3.0441      0.1530
>     942    941   88.6    0.1297   0.2327      0.1530
>     943    944   93.1    0.1291  20.4158      0.1530
>     944    945   93.6    0.1491 116.4443      0.1530
> ................................
>             Wrote pdb files with previous and current coordinates
> -----------------------------------------------------------------------------
> One of the processes started by mpirun has exited with a nonzero exit
> code.  This typically indicates that the process finished in error.
> If your process did not finish in error, be sure to include a "return
> 0" or "exit(0)" in your C code before exiting the application.
> 
> PID 21625 failed on node n0 (127.0.0.1) due to signal 11.
> -----------------------------------------------------------------------------

http://wiki.gromacs.org/index.php/Errors#Pressure_scaling_more_than_1.25

Mark