Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected"

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Thu Sep 13 2007 - 05:01:18 CDT

Hi,

I have a 110 x 110 x 170 A bilayer (build using vmd plugins), which I am
trying to minimize using a PME grid of 120 x 120 x 180. However, starting
from minimization step 80, I get several errors similar to the following in
the simulation

##############################
..
ERROR: Stray PME grid charges detected: 28 sending to 25 for planes 92 93 94
95
ERROR: Stray PME grid charges detected: 28 sending to 10 for planes 36 37 38
39
##############################

Eventually the simulation crashes with the log:

##############################
..

ERROR: Stray PME grid charges detected: 28 sending to 23 for planes 84 85 86
87
Stack Traceback:
  [0] _ZN17ComputeHomeTuplesI8BondElem4bond9BondValueE10loadTuplesEv+0x95e
[0x81311ae]
  [1] _ZN17ComputeHomeTuplesI8BondElem4bond9BondValueE6doWorkEv+0x56b
[0x8133b7b]
  [2] _ZN11WorkDistrib12enqueueBondsEP12LocalWorkMsg+0x19 [0x82de0ed]
  [3]
_ZN19CkIndex_WorkDistrib31_call_enqueueBonds_LocalWorkMsgEPvP11WorkDistrib+0x11
[0x82de0cd]
  [4] CkDeliverMessageFree+0x29 [0x8322f7d]
  [5] _Z15_processHandlerPvP11CkCoreState+0x417 [0x83225bf]
  [6] CmiHandleMessage+0x1d [0x837c885]
  [7] _ZN7BackEnd4initEiPPc+0x295 [0x80e2f89]
  [8] main+0x30 [0x80deff4]
  [9] __libc_start_main+0xdc [0xf7d3c87c]
  [10] _ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_c+0x59
[0x80dba71]
##############################

Looking at the trajectory (3 frames, 5000 steps of minimization each),
several atoms have moved out of the simulation box, and have very long bonds
with atoms inside the box. These are both POPC and water atoms.

Can someone please tell me what the issue might be ?

Thank you very much,

-- 
Maria G.
Technical University of Denmark
Copenhagen

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:46:58 CST