RE: autoionize & namd2

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Sep 21 2005 - 02:24:09 CDT

Hi,
 
In this case, the charge is not a problem, since it's "close" to zero. The problem should be in your simulation script. Maybe you're not correctly setting the periodic boundary conditions; it's my guess (just looking at the energies during the minimization).
On the other hand, a assume that you're equilibrating your system before the real simulation. so pay attention to that, as well.
I recommend you to check your simulation script and the size of your cell (you can easily do that with vmd), and re-run your simulation.
Hope it helps,
Michel

________________________________

From: owner-namd-l_at_ks.uiuc.edu on behalf of bo baker
Sent: Tue 9/20/2005 6:07 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: autoionize & namd2

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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