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
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