From: paul.dalhaimer_at_yale.edu
Date: Wed Sep 21 2005 - 09:47:37 CDT
I used the commands separately.
>package require autoionize
>autoionize -psf protein_water.psf -pdb protein_water.pdb -is 0.1 -o
protein_water_salt
then vmd crashed. It also crashed with
>autoionize -psf protein_water.psf -pdb protein_water.pdb -nna 50 -ncl
50 -o protein_water_salt
I tried variations on the ionic strength and number of ions. No luck.
Quoting Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu>:
> 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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