From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Sep 21 2005 - 09:32:45 CDT
when you used the -is option, autoionize or vmd crashed? you can try to use -nna and -ncl together if you know the net charge of your system (e.g. -nna 2 -ncl 0, assuming that you only want to get a neutral system), but don't use -nxx + the -is options together... make me know if it worked.
Michel
________________________________
From: paul.dalhaimer_at_yale.edu [mailto:paul.dalhaimer_at_yale.edu]
Sent: Wed 9/21/2005 9:19 AM
To: Michel Espinoza-Fonseca
Subject: RE: namd-l: autoionize & namd2
Also, has any one had problems ionizing large water boxes? I tried to
ionize a simulation with ~150,000 water molecules and two proteins and
it crashed whether I used the -nna or -is options.
Quoting Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu>:
> 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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