From: Cartailler, Jean-Philippe (jp.cartailler_at_Vanderbilt.Edu)
Date: Thu Oct 02 2003 - 11:17:58 CDT
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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