[gmx-users] LINCS warnings (6153)

[David van der Spoel]

Ernesto Andres Román wrote:
> Dear gmx-user,
>                            Im just making my first moves in protein 
> dynamics simulation. Ive done some tutorials and peptide-water 
> simulations. But now im intending to change the solvent to CCL4. Ive got 
> the solvent parameters, made the topology file, and the .gro file with 
> the solvent and peptide together. When I run mdrun commando an error 
> message displays:

did you do a separate CCl4 simulation?
you can probably also up the other lincs flags.


> Fatal error:
> Too many LINCS warnings (6153)
> If you know what you are doing you can adjust the lincs warning 
> threshold in your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem
> 
> My .mdp file is:
> define              = -DFLEXIBLE
> constraints         = none
> integrator          = steep
> dt                  = 0.002     ; ps !
> nsteps              = 400
> nstlist             = 10
> ns_type             = grid
> rlist               = 1.0
> coulombtype         = PME
> rcoulomb            = 1.0
> vdwtype             = cut-off
> rvdw                = 1.4
> fourierspacing          = 0.12
> fourier_nx        = 0
> fourier_ny        = 0
> fourier_nz        = 0
> pme_order         = 4
> ewald_rtol        = 1e-5
> optimize_fft            = yes
> ;
> ;       Energy minimizing stuff
> ;
> emtol               = 1000.0
> emstep              = 0.01
> 
> Do you know what could be happening, and more important, how to solve it 
> or where to look for the problem ?
> Thanks,
> Ernesto.
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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