[gmx-users] mdrun error after 2.6nS

[Tsjerk Wassenaar]

Hi Blaise,

You'd better look in the log file where this starts. I bet it's either
Lys-NH3+ or phosphate (ATP?) spinning like crazy. Check the archive for
solutions.

Best,

Tsjerk

On 10/2/07, Blaise Mathias-Costa <bmathiascosta at unmc.edu> wrote:
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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