normal Reverse transformation not working for higher number of steps

  • Rajat Desikan
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11 years 10 months ago #964 by Rajat Desikan
Hi
I have a problem. The reverse transformation for my membrane-protein-water system worked well for 1000 steps and SA time step of 0 1.5 0 1.5 0 1.5 When I increased the steps to 5000 and SA timestep to 0 7.5 0 7.5 0 7.5 , it crashes with the following error:

Step 3397, time 6.794 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.347253 (between atoms 854598 and 854599) rms 0.002481
bonds that rotated more than 100 degrees:
atom 1 atom 2 angle previous, current, constraint length

Step 3398, time 6.796 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.287802 (between atoms 613449 and 613451) rms 0.002476
bonds that rotated more than 100 degrees:
atom 1 atom 2 angle previous, current, constraint length

Step 3399, time 6.798 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 0.324448 (between atoms 854598 and 854599) rms 0.002479
bonds that rotated more than 100 degrees:
atom 1 atom 2 angle previous, current, constraint length

Program mdrun_mpi, VERSION 3.3.1
Source code file: stat.c, line: 257

Fatal error:
XTC error

"Bailed Out Of Edge Synchronization After 10,000 Iterations" (X/Motif)

Halting program mdrun_mpi

gcq#237: "Bailed Out Of Edge Synchronization After 10,000 Iterations" (X/Motif)

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode -1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
[/b]

What should I do?

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11 years 10 months ago #967 by djurre
To me, there is no obvious reason why the second simulation crashes. It might be you just got unlucky. Could you try again with different starting velocities? (mdp-file: gen_vel = yes, gen_seed = 234524)

Just to be sure: did you start the latter simulation from the output of the 1000 step simulation, or from the initial starting files? (it should be the second, the goal of the exercise is to compare the different runs).

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11 years 10 months ago #968 by Rajat Desikan
Hi Djurre
I started the second simulation from the initial starting files. I will try a different seed and update you guys. Thanks for the response

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11 years 10 months ago #973 by Rajat Desikan
Hi Djurre
Using a different seed worked :)...thanks

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