[gmx-users] AGAIN fatal error:determinant in mdrun
Osmany Guirola Cruz
osmany.guirola at cigb.edu.cu
Mon Jul 28 22:43:01 CEST 2003
David this is the ouput of my mdrun the energy values are not close to
zero Where is the problem , what can i do?
Step Time Lambda Annealing
440 440.00000 0.00000 0.00000
Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
8.79365e+03 6.07128e+03 2.18208e+03 1.18862e+02 -6.92091e+02
Coulomb-14 LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR)
4.05097e+03 9.32364e+03 -1.64323e+03 -2.47540e+05 -6.10418e+03
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-2.25439e+05 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00
Step Time Lambda Annealing
441 441.00000 0.00000 0.00000
Step Time Lambda Annealing
442 442.00000 0.00000 0.00000
Stepsize too small (6.86046e-07 nm)Converged to machine precision,
but not to the requested precision (100)
Steepest Descents did not converge in 443 steps
Potential Energy = -2.25439e+05
Maximum force: 3.57473e+03
The energy values are not CLOSE to zero WHAT CAN I DO
THIS IS MY EM.MDP FILE
define = -DFLEX_SPC
constraints = none
integrator = steep
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
>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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