From: lecan (lecan_at_ibt.unam.mx)
Date: Fri May 04 2012 - 00:19:38 CDT
Hello everybody.
I was trying to run a MD with a solvated protein without any restrain.
After energy minimization I got the message:
OPENING EXTENDED SYSTEM TRAJECTORY FILE
FATAL ERROR: Periodic cell has become too small for original patch
grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
UseFlexibleCell is disabled. So I minimized again, but this time with
an iterative protocol. I used twenty iterations during minimization, but
yet obtained this.
Info: PATCH GRID IS 4 (PERIODIC) BY 6 (PERIODIC) BY 4 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
After these I increase margin to 1.5 (default was 0.48), and then I got
this other message:
OPENING EXTENDED SYSTEM TRAJECTORY FILE
ERROR: Atom 1409 velocity is -32354 6187.9 30795.9 (limit is 6000, atom
0 of 687 on patch 10 pe 0)
ERROR: Atom 1412 velocity is 1445.89 -13205.7 36440.7 (limit is 6000,
atom 1 of 687 on patch 10 pe 0)
ERROR: Atom 1414 velocity is -14451.4 10761 32904.3 (limit is 6000,
atom 3 of 687 on patch 10 pe 0)
For many atoms, not only these three ones.
With these new margin the patch grid do change:
Info: PATCH GRID IS 4 (PERIODIC) BY 5 (PERIODIC) BY 4 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
but now I got this speed limit exceed.
When I visualize the system with VMD everything looks OK.
Does anyone can help me with this problem?
Luis L.
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