RE: autoionize & namd2

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Sep 22 2005 - 02:51:08 CDT

Hi Bo,
 
I just checked your script and I found some important mistakes. Your script does not follow the "normal" pathway towards a successful equilibration of your system, and you're getting this error because you're almost avoiding the heating process, so the atoms are moving too fast.
Attached please find a script template that might be useful for your equilibrations. You will need a 2 more pdb's. You can modify some of the parameters, but you have to add on it the information of YOUR system.
Take a look to the following webpage: http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/
You'll find useful things there, including how to create the 2 extra pdb files you need.
Hope it helps,
Michel

________________________________

From: bo baker [mailto:bo.bybaker_at_gmail.com]
Sent: Wed 9/21/2005 6:56 PM
To: Michel Espinoza-Fonseca
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: autoionize & namd2

Hi,

Thanks for your suggestions.

I use VMD to check the max size of my cell, and add them to the .conf
script. The the run didn't go through. The same probelm as before. My
run scrip is based on the NAMD tutorial (ubq_wb.conf). I have
included my .conf and .log files as attachments.

Can anyone help me to figure out what was wrong with my script?

Thank you very much

Bo

On 9/21/05, Michel Espinoza-Fonseca <mef_at_ddt.biochem.umn.edu> wrote:
> 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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