[gmx-users] AGAIN fatal error:determinant in mdrun

[David]

On Mon, 2003-07-28 at 20:53, Osmany Guirola Cruz wrote:
> I have the same error in my simulation
> i do a em step whitout problem but when i begin the md(whitout define = 
> -DPOSRES)simulations i have problem whith Lincs
> i probe use shake but the method not converge ,
> Please  what i have to do whith my mdp files for a GREAT SIMULATION
>     thanks'


such problems come from bad starting structures usually. Did you check
that all bond and angle energies are close to zero after minimizing?

> 
> nanyu101 wrote:
> 
> >Dear gmx-users,
> >  I have created a bigger lipid bilayer with genconf.
> >genconf -f popc128a.pdb -nbox 2 2 1 -dist 0 0 0 -o popc.pdb
> >
> >And this bilayer is as big as four times of former bilayer.After doing that, I have run minimization for this big bilayer with cut-off for long distance electrostatic.
> > title               =  Yo
> >cpp                 =  /lib/cpp
> >define              =  -DPOSRES
> >constraints         =  none
> >integrator          =  steep
> >emstep              =  0.001
> >emtol               =  10
> >nsteps              =  200000
> >nstcomm             =  1
> >nstxout             =  50
> >nstvout             =  1000
> >nstfout             =  0
> >nstlog              =  10
> >nstenergy           =  10
> >nstlist             =  10
> >pbc                 =  xyz
> >ns_type             =  grid
> >coulombtype         =  cut-off
> >rlist               =  1.2
> >rcoulomb            =  1.8
> >rvdw                =  1.4
> >Tcoupl              =  no
> >Pcoupl              =  no                              
> >gen_vel             =  no
> > 
> >
> >After minimizing my big bilayer,I tried to run NPT, but the system told me this:
> >Using Gromacs SSE single precision assembly innerloops.
> >
> >           Step           Time         Lambda      Annealing
> >              0        0.00000        0.00000        1.00000
> >
> >   Rel. Constraint Deviation:  Max    between atoms     RMS
> >       Before LINCS         0.004860  47622  47624   0.000779
> >        After LINCS         0.000078  19562  19563   0.000009
> >
> >Fatal error: Determinant = 1325213994729268314112.000000
> >
> >
> >My operation mdp file and commands are listed as follows.
> >cpp                 =  /lib/cpp
> >define              =  -DPOSRES
> >constraints         =  all-bonds
> >integrator          =  md
> >dt                  =  0.002	; ps !
> >nsteps              =  10000
> >nstcomm             =  1
> >comm_mode           =  angular
> >nstxout             =  50
> >nstvout             =  1000
> >nstfout             =  0
> >nstlog              =  10
> >nstenergy           =  10
> >nstlist             =  10
> >pbc                 =  xyz
> >ns_type             =  grid
> >coulombtype         =  cut-off
> >fourierspacing      = 0.12
> >optimize_fft        = yes
> >rlist               =  1.0
> >rcoulomb            =  1.8
> >rvdw                =  1.4
> >Tcoupl              =  no
> >Pcoupl              =  berendsen
> >pcoupltype          =  anisotropic                              
> >tau_p               =  1   1   1   0   0   0
> >compressibility     =  4.5e-5  4.5e-5  4.5e-5  0.0  0.0  0.0
> >ref_p               =  1   1  1  0  0  0
> >gen_vel             =  yes
> >gen_temp            =  325.0
> >gen_seed            =  1
> > 
> >
> >editconf -f popc.pdb -o popc.gro
> >editconf -bt cubic -f popc.gro -o popc.gro -c -center 0 0 0 -rotate 0 0 0
> >grompp -f md.mdp -c popc.gro -p popc.top -o popc.tpr
> >mdrun -v -deffmn popc
> >
> >
> >Any comments are recommended. Thanks a lot.
> >
> >best wishes,
> >Xianhui Wu
> >
> >
> > 
> >______________________________________
> >
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> >  
> >
> 
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel
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