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

[David]

On Tue, 2003-07-29 at 00:12, Osmany Guirola Cruz wrote:
> David  My starting structures are from the web site
> moose.bio.ucalgary.ca 
> i get the pdb file  ,then i convert it to GRO format , do an energy
> minimization(withouy problem)
> an then the MD ,HOW can i check that all bond and angle energies are
> close to zero after the EM?
> 
> THANKS
in the md.log file that you get from the minimization. Do you use
confout.gro from EM for the MD?

> 
> 
> 
> 
> David wrote:
> > 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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