[gmx-users] mdrun error after 2.6nS

Tue, 02 Oct 2007 09:38:04 -0700

Hi all,

The mdrun stopped  after 2.6nS  after writing this error:
Step 1321571, time 2643.14 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 2.814066 (between atoms 2742 and 2745) rms 0.041434
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
  2742   2743   90.1    0.1728   0.0946      0.1000
  2742   2744   90.0    0.1010   0.2410      0.1000
  2742   2745   90.0    0.1675   0.3814      0.1000

like this for 100s of times..

here is the md.mdp file:
cpp                      = cpp
include                  = -I../top
define                   =
integrator              = md
dt                        = 0.002
comm_grps            = Protein
nstcomm               = 1
nsteps                  = 2500000
nstxout                 = 5000
nstvout                 = 5000
nstlog                   = 5000
nstenergy              = 500
nstxtcout               = 250
xtc_grps                 = Protein
energygrps              = Protein non-protein
nstlist                    = 10
 

Blaise Mathias Costa, PhD
Department of Pharmacology and Experimental Neuroscience
University of Nebraska Medical Center
Omaha, NE 68198-5800, USA.
Tel: 001 402 559 7132 
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