[gmx-users] AGAIN fatal error:determinant in mdrun
David
spoel at xray.bmc.uu.se
Mon Jul 28 21:47:01 CEST 2003
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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--
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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