From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Oct 03 2003 - 13:09:35 CDT
Hi,
Your BOUNDARY energy is huge (over 7M kcal/mol) and 100 steps of
minimization is too short to deal with this assuming it is correct.
I assume that your spherical boundary conditions are somehow wrong:
# Spherical boundary conditions
sphericalBC on
sphericalBCcenter 51.2431388091 76.9359234446 -17.1876324976
sphericalBCr1 26.0
sphericalBCk1 10
sphericalBCexp1 2
Perhaps the center or radius of your system is not specified properly?
My rule of thumb is 1 atom per 10 cubic Angstroms, so a radius of 26 A
would allow 7362 atoms to fit in the sphere. You have 20928 in your
simulation, so the radius of the sphere is too small. 36 A would be about
the right size, so maybe this is a typo.
Try saving a DCD file at every step and looking at it in VMD, this should
show rather clearly which atoms are being affected. Fix this, and try
minimizing for 1000 steps before starting dynamics.
-Jim
On Thu, 2 Oct 2003, Cartailler, Jean-Philippe wrote:
> Hello list,
>
> I am a new NAMD user and am following the manual and the tutorials to learn NAMD just to accomplish a 'small' project, i.e. to shake around a homology model (nothing fancy, no cofactors, etc.).
>
> Instead of attaching the relevant conf and log files of my NAMD simulation, I have put these online:
>
> http://structbio.vanderbilt.edu/~jp/tmp/namd/alpha3_ws_eq.conf
> http://structbio.vanderbilt.edu/~jp/tmp/namd/alpha3_ws_eq.log
>
> The simulation becomes unstable:
>
> (in log file)...
> REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN.
> TCL: Running for 5000 steps
> ERROR: Constraint failure in RATTLE algorithm for atom 331!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely.
>
> atom 331 is a LEU CD1. I checked the PDB and PSF files, against those from tutorial files and that atom appears normal in those files. There is also a warning in the log file:
>
> Warning: Bad global exclusion count, possible error!
> Warning: Increasing cutoff during minimization may avoid this.
>
> I tried increasing the cutoff for the "Force-Field Parameters" from 12 to 15 (along with an increase of the pairlistdist > cutoff), but this did not help.
>
> I have followed the "NAMD tutorial" (http://www.ks.uiuc.edu/Training/SumSchool/materials/sources/tutorials/02-namd-tutorial/namd-tutorial-html/) successfully for the model protein. I imagine that certain parameters need to be tweaked to make this work for my protein. If anyone can advise a newbie like myself on what the problem might be, that'd be great.
>
> Thank you,
>
> JP Cartailler
>
>
>
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