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

From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Thu Sep 13 2007 - 08:00:09 CDT

Hi all, I'm not that familiar with PME grids, but it seems to me that the grid in this situation might be too small? I jnow that when I used to work with solvated systems we would try and have at least 10A around all the "sides" of the solute so that it wouldn't stick out of the water. Perhaps that is what is happening here, as you have a 5A clearance on each end between your system and the grid? Richard Richard L. Wood, Ph. D. University of Minnesota Dept. of Medicinal Chemistry, College of Pharmacy 717 Delaware St. SE Minneapolis, MN 55414-2959 rwoodphd_at_yahoo.com ----- Original Message ---- From: maria goranovic <mariagoranovic_at_gmail.com> To: NAMD list <namd-l_at_ks.uiuc.edu> Sent: Thursday, September 13, 2007 6:01:18 AM Subject: namd-l: Simulation of large bilayer crashes with "ERROR: Stray PME grid charges detected" 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 ____________________________________________________________________________________ Catch up on fall's hot new shows on Yahoo! TV. Watch previews, get listings, and more! http://tv.yahoo.com/collections/3658

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