From: bo baker (bo.bybaker_at_gmail.com)
Date: Tue Sep 20 2005 - 18:07:34 CDT
Hello, NAMD:
I try to neutralize the system by using 'autoionize' command. One
thing is that the program calculate the system net charge before
adding ions is '-1.99999714395e'. And after add ions, the net charge
is '2.85605666939e-06e', not zero. Here is how I did:
---- Autoionize) Reading N62-1_wb.psf/N62-1_wb.pdb... reading structure from psf file N62-1_wb.psf reading coordinates from pdb file N62-1_wb.pdb Autoionize) System net charge before adding ions: -1.99999714395e Autoionize) Desired ion concentration 0.05 mol/L Autoionize) Adding 5 Na and 3 Cl ions, total 8 ions Autoionize) Required min distance from molecule 5A Autoionize) Required min distance between ions 5A Autoionize) Output file prefix 'ionized' Autoionize) Obtained positions for 8 ions Autoionize) Tagged 8 water molecules for deleting Autoionize) Deleted 8 water molecules Autoionize) Adding 5 SOD and 3 CLA residues... building segment ION setting patch for first residue to NONE setting patch for last residue to NONE Info: generating structure... Info: segment complete. Autoionize) Randomizing ion positions... Autoionize) Assigned 5 Na coordinates Autoionize) Assigned 3 Cl coordinates Info: writing psf file ionized.psf total of 29120 atoms total of 20563 bonds total of 14768 angles total of 9033 dihedrals total of 580 impropers Info: psf file complete. Info: writing pdb file ionized.pdb Info: pdb file complete. Autoionize) Reloading the system with added ions... Autoionize) System net charge after adding ions: 2.85605666939e-06e Autoionize) All done. ------- When I subjected the ionized system for namd2 run, it showed strange energy levels as 'ENERGY: 1 196985.3140 27944.2341 1172.0142 606.2699 -9475.4324 99999999.9999 0.0000 0.0000 0.0000 99999999.9999 0.0000 99999999.9999 99999999.9999 0.0000 99999999.9999 99999999.9999 86856.0000 99999999.9999 99999999.9999' And eventually, the program stopped as: REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN. TCL: Running for 2500 steps ERROR: Constraint failure in RATTLE algorithm for atom 1212! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 557! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 1094! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 916! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 498! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 470! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 5! ERROR: Constraint failure; simulation has become unstable. ERROR: Constraint failure in RATTLE algorithm for atom 10! ERROR: Constraint failure; simulation has become unstable. ERROR: Exiting prematurely. ========================================== WallClock: 4195.953125 CPUTime: 4185.009766 Memory: 0 kB Program finished. [1] + Exit 1 I am not sure if the net charge of system caused the failture of equiliration with namd2. I use NAMD_2.6b1_MacOSX-PPC. The .psf and .pdb filea were generated by using VMD.1.8.3. Thanks for any comments. Bo
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