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

From: Philip Peartree (P.Peartree_at_postgrad.manchester.ac.uk)
Date: Thu Sep 13 2007 - 07:24:42 CDT

I assume you're running in full periodic boundary conditions? Could you
post the
input script you're using?

Philip Peartree

Quoting maria goranovic <mariagoranovic_at_gmail.com>:

> 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
>

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