Large MD simulations and atom number limits with NAMD

From: Andrew Thomas (asthomas99_at_hotmail.com)
Date: Fri Jun 20 2008 - 09:53:50 CDT

Dear all,
 
I am interested in running very large MD simulations (>4 million atoms). I have read a previous post suggesting that NAMD is limited to ~4 million atoms due to the use of 22-bit atom IDs. I was wondering if there was a workaround for this limitation. For testing I've set up different boxes of waters all setup using the same scripts:
0) small systems 100k to 3.9 million atoms work fine, no problems,
1) a system with 4.29 millions atoms gives the error:
################
Info: Entering startup phase 0 with 1886724 kB of memory in use.Info: Entering startup phase 1 with 1886724 kB of memory in use.Info: Entering startup phase 2 with 2893392 kB of memory in use.Info: Entering startup phase 3 with 2926956 kB of memory in use.Info: PATCH GRID IS 20 (PERIODIC) BY 20 (PERIODIC) BY 20 (PERIODIC)Info: REMOVING COM VELOCITY 0.00477832 -0.00342197 -0.000182436FATAL ERROR: Mother atom with hydrogenGroupSize of 0!FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html------------- Processor 0 Exiting: Called CmiAbort ------------################
2) a system with 12.5 million atoms gives a Segmentation fault:
################
Info: COORDINATE PDB test.pdbInfo: STRUCTURE FILE final.2.psfInfo: PARAMETER file: CHARMM format!Info: PARAMETERS /home/athomas/toppar/par_all27_prot_lipid.prmInfo: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERSInfo: SUMMARY OF PARAMETERS:Info: 180 BONDSInfo: 447 ANGLESInfo: 566 DIHEDRALInfo: 46 IMPROPERInfo: 6 CROSSTERMInfo: 114 VDWInfo: 0 VDW_PAIRSSegmentation fault################
 
Memory does not seem to be the problem; I'm working on a 24 GB system and memory only goes to ~ 10-20% before crashing.
 
Any help would be most appreciated, I've searched the archives as well as net searches and I've not seen a solution. I presume there is some fix for this as Klaus Schulten is looking towards simulations well over the 4million atom limit.
 
Andy Thomas, Ph.D.
Dept. Biochemistry
University of Iowa
 
 
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