[gmx-users] table force-field

Tue Aug 5 14:05:19 CEST 2008

2008/8/5 Justin A. Lemkul <jalemkul at vt.edu>

>
>  Yes I done energy minimization, and mdrun output here:
>> Steepest Descents converged to machine precision in 17 steps,
>> but did not reach the requested Fmax < 10.
>> Potential Energy = -1.6686725e+06
>> Maximum force = 2.4212272e+07 on atom 5
>> Norm of force = 3.4130568e+07
>>
>
> This would concern me a bit.  You've got an enormous force on atom 5!
>  That's probably causing the explosion.  So even though the potential energy
> seems reasonable, you've got something pushing very hard against that
> particle, and it may be ripping your system apart.
>
> You were aiming for an Fmax < 10, and got nowhere close (by a factor of a
> million!) so I would check that initial configuration and examine your
> parameters closely.
>
> -Justin
>
>  other files from my system here too. It is chain cosist 5 coarse-grained
>> units, in initial conformation there are two parallel chains on distance
>>  nm.
>> ==============ffgmx.itp======================== [ defaults ]
>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>>  1 1 no 1.0 1.0
>>
>> [ atomtypes ]
>>
>>  B 337.000 0.000 A 4.275 2.14
>> [ bondtypes ]
>> ; i j func b0 kb
>>  B B 1 1.3 1105.7 ; gaussian
>> [ angletypes ]
>>  B B B 1 170.7 33.4
>> [ dihedraltypes ]
>>  B B B B 1 164.9 0.87 1
>> [ nonbond_params ]
>> ;i j C6 C12
>>  B B 1 4.275 2.14
>>
>> [ pairtypes ]
>> ;i j C6 C12
>>  B B 1 4.275 2.14
>>
>> =====================table.xvg===============================
>>
>> 0 0.0 0.0 5.31525e-317 0.0 0.0 0.0
>> 0.0505051 0.0 0.0 2.72297e 0.0 0.0 0.0
>> 0.10101 0.0 0.0 6.64787e 0.0 0.0 0.0
>> 0.151515 0.0 0.0 5.12363e 0.0 0.0 0.0
>> 0.20202 0.0 0.0 1.6228e 0.0 0.0 0.0
>> 0.252525 0.0 0.0 1.11475e 0.0 0.0 0.0
>> 0.30303 0.0 0.0 1.24898e 0.0 0.0 0.0
>> 0.353535 0.0 0.0 195960 0.0 0.0 0.0
>> 0.40404 0.0 0.0 39279.7 0.0 0.0 0.0
>> 0.454545 0.0 0.0 9471.18 0.0 0.0 0.0
>> 0.505051 0.0 0.0 2632.59 0.0 0.0 0.0
>> 0.555556 0.0 0.0 816.605 0.0 0.0 0.0
>> 0.606061 0.0 0.0 275.131 0.0 0.0 0.0
>> 0.656566 0.0 0.0 98.1504 0.0 0.0 0.0
>> 0.707071 0.0 0.0 36.0257 0.0 0.0 0.0
>> 0.757576 0.0 0.0 13.0521 0.0 0.0 0.0
>> 0.808081 0.0 0.0 4.28676 0.0 0.0 0.0
>> 0.858586 0.0 0.0 0.929196 0.0 0.0 0.0
>> 0.909091 0.0 0.0 -0.30352 0.0 0.0 0.0
>> 0.959596 0.0 0.0 -0.690878 0.0 0.0 0.0
>> 1.0101 0.0 0.0 -0.747432 0.0 0.0 0.0
>> 1.06061 0.0 0.0 -0.683641 0.0 0.0 0.0
>> 1.11111 0.0 0.0 -0.585339 0.0 0.0 0.0
>> 1.16162 0.0 0.0 -0.486288 0.0 0.0 0.0
>> 1.21212 0.0 0.0 -0.398389 0.0 0.0 0.0
>> 1.26263 0.0 0.0 -0.324521 0.0 0.0 0.0
>> 1.31313 0.0 0.0 -0.264044 0.0 0.0 0.0
>> 1.36364 0.0 0.0 -0.21515 0.0 0.0 0.0
>> 1.41414 0.0 0.0 -0.175831 0.0 0.0 0.0
>> 1.46465 0.0 0.0 -0.144252 0.0 0.0 0.0
>> 1.51515 0.0 0.0 -0.118857 0.0 0.0 0.0
>> 1.56566 0.0 0.0 -0.0983815 0.0 0.0 0.0
>> 1.61616 0.0 0.0 -0.0818131 0.0 0.0 0.0
>> 1.66667 0.0 0.0 -0.0683514 0.0 0.0 0.0
>> 1.71717 0.0 0.0 -0.0573661 0.0 0.0 0.0
>> 1.76768 0.0 0.0 -0.0483612 0.0 0.0 0.0
>> 1.81818 0.0 0.0 -0.0409463 0.0 0.0 0.0
>> 1.86869 0.0 0.0 -0.0348131 0.0 0.0 0.0
>> 1.91919 0.0 0.0 -0.0297176 0.0 0.0 0.0
>> 1.9697 0.0 0.0 -0.025466 0.0 0.0 0.0
>> 2.0202 0.0 0.0 -0.0219036 0.0 0.0 0.0
>> 2.07071 0.0 0.0 -0.0189067 0.0 0.0 0.0
>> 2.12121 0.0 0.0 -0.0163756 0.0 0.0 0.0
>> 2.17172 0.0 0.0 -0.0142297 0.0 0.0 0.0
>> 2.22222 0.0 0.0 -0.0124039 0.0 0.0 0.0
>> 2.27273 0.0 0.0 -0.010845 0.0 0.0 0.0
>> 2.32323 0.0 0.0 -0.00950938 0.0 0.0 0.0
>> 2.37374 0.0 0.0 -0.00836141 0.0 0.0 0.0
>> 2.42424 0.0 0.0 -0.00737164 0.0 0.0 0.0
>> 2.47475 0.0 0.0 -0.00651568 0.0 0.0 0.0
>> 2.52525 0.0 0.0 -0.0057733 0.0 0.0 0.0
>> 2.57576 0.0 0.0 -0.00512764 0.0 0.0 0.0
>> 2.62626 0.0 0.0 -0.00456457 0.0 0.0 0.0
>> 2.67677 0.0 0.0 -0.00407227 0.0 0.0 0.0
>> 2.72727 0.0 0.0 -0.00364076 0.0 0.0 0.0
>> 2.77778 0.0 0.0 -0.00326162 0.0 0.0 0.0
>> 2.82828 0.0 0.0 -0.00292772 0.0 0.0 0.0
>> 2.87879 0.0 0.0 -0.002633 0.0 0.0 0.0
>> 2.92929 0.0 0.0 -0.00237231 0.0 0.0 0.0
>> 2.9798 0.0 0.0 -0.00214121 0.0 0.0 0.0
>> 3.0303 0.0 0.0 -0.00193595 0.0 0.0 0.0
>> 3.08081 0.0 0.0 -0.00175327 0.0 0.0 0.0
>> 3.13131 0.0 0.0 -0.00159038 0.0 0.0 0.0
>> 3.18182 0.0 0.0 -0.00144487 0.0 0.0 0.0
>> 3.23232 0.0 0.0 -0.00131466 0.0 0.0 0.0
>> 3.28283 0.0 0.0 -0.00119792 0.0 0.0 0.0
>> 3.33333 0.0 0.0 -0.0010931 0.0 0.0 0.0
>> 3.38384 0.0 0.0 -0.000998824 0.0 0.0 0.0
>> 3.43434 0.0 0.0 -0.000913896 0.0 0.0 0.0
>> 3.48485 0.0 0.0 -0.000837272 0.0 0.0 0.0
>> 3.53535 0.0 0.0 -0.000768038 0.0 0.0 0.0
>> 3.58586 0.0 0.0 -0.000705391 0.0 0.0 0.0
>> 3.63636 0.0 0.0 -0.000648625 0.0 0.0 0.0
>> 3.68687 0.0 0.0 -0.000597116 0.0 0.0 0.0
>> 3.73737 0.0 0.0 -0.000550316 0.0 0.0 0.0
>> 3.78788 0.0 0.0 -0.00050774 0.0 0.0 0.0
>> 3.83838 0.0 0.0 -0.000468957 0.0 0.0 0.0
>> 3.88889 0.0 0.0 -0.000433586 0.0 0.0 0.0
>> 3.93939 0.0 0.0 -0.000401288 0.0 0.0 0.0
>> 3.9899 0.0 0.0 -0.000371763 0.0 0.0 0.0
>> 4.0404 0.0 0.0 -0.000344741 0.0 0.0 0.0
>> 4.09091 0.0 0.0 -0.000319982 0.0 0.0 0.0
>> 4.14141 0.0 0.0 -0.000297274 0.0 0.0 0.0
>> 4.19192 0.0 0.0 -0.000276423 0.0 0.0 0.0
>> 4.24242 0.0 0.0 -0.000257258 0.0 0.0 0.0
>> 4.29293 0.0 0.0 -0.000239626 0.0 0.0 0.0
>> 4.34343 0.0 0.0 -0.000223388 0.0 0.0 0.0
>> 4.39394 0.0 0.0 -0.000208419 0.0 0.0 0.0
>> 4.44444 0.0 0.0 -0.000194607 0.0 0.0 0.0
>> 4.49495 0.0 0.0 -0.000181851 0.0 0.0 0.0
>> 4.54545 0.0 0.0 -0.00017006 0.0 0.0 0.0
>> 4.59596 0.0 0.0 -0.000159152 0.0 0.0 0.0
>> 4.64646 0.0 0.0 -0.000149051 0.0 0.0 0.0
>> 4.69697 0.0 0.0 -0.00013969 0.0 0.0 0.0
>> 4.74747 0.0 0.0 -0.000131008 0.0 0.0 0.0
>> 4.79798 0.0 0.0 -0.000122948 0.0 0.0 0.0
>> 4.84848 0.0 0.0 -0.000115462 0.0 0.0 0.0
>> 4.89899 0.0 0.0 -0.000108502 0.0 0.0 0.0
>> 4.94949 0.0 0.0 -0.000102026 0.0 0.0 0.0
>> 5 0.0 0.0 -9.59969e-05 0.0 0.0 0.0
>>
>> =================================grompp.mdp====================
>>
>>
>> ; File 'mdout.mdp' was generated
>> ; By user: spoel (291)
>> ; On host: chagall
>> ; At date: Mon Dec 15 13:52:23 2003
>> ;
>>
>> ; VARIOUS PREPROCESSING OPTIONS
>> title = Perylene
>> ;cpp = xlc -E
>> cpp = cpp
>> include =
>> define =
>>
>> ; RUN CONTROL PARAMETERS
>> integrator = steep
>> ; Start time and timestep in ps
>> tinit = 0
>> dt = 0.002
>> nsteps = 10000  ; For exact run continuation or redoing part of a run
>> init_step = 0
>> ; mode for center of mass motion removal
>> ;comm-mode = None
>> comm-mode = Linear
>> ;comm-mode = Angular
>> ; number of steps for center of mass motion removal
>> nstcomm = 1
>> ; group(s) for center of mass motion removal
>> comm-grps =
>>
>> ; LANGEVIN DYNAMICS OPTIONS
>> ; Temperature, friction coefficient (amu/ps) and random seed
>> bd-fric = 0.5
>> ld-seed = 1993
>>
>> ; ENERGY MINIMIZATION OPTIONS
>> ; Force tolerance and initial step-size
>> emtol = 10
>> emstep = 0.01
>> ; Max number of iterations in relax_shells
>> niter = 2000
>> ; Step size (1/ps^2) for minimization of flexible constraints
>> fcstep = 0
>> ; Frequency of steepest descents steps when doing CG
>> nstcgsteep = 1000
>> nbfgscorr = 10
>>
>> ; OUTPUT CONTROL OPTIONS
>> ; Output frequency for coords (x), velocities (v) and forces (f)
>> nstxout = 10000
>> nstvout = 0
>> nstfout = 0
>> ; Checkpointing helps you continue after crashes
>> nstcheckpoint = 10000
>> ; Output frequency for energies to log file and energy file
>> nstlog = 10000
>> nstenergy = 10000
>> ; Output frequency and precision for xtc file
>> nstxtcout = 100
>> xtc-precision = 1000
>> ; This selects the subset of atoms for the xtc file. You can
>> ; select multiple groups. By default all atoms will be written.
>> xtc-grps =
>> ; Selection of energy groups
>> energygrps =
>>
>> ; NEIGHBORSEARCHING PARAMETERS
>> ; nblist update frequency
>> nstlist = 5
>> ; ns algorithm (simple or grid)
>> ns_type = grid
>> ; Periodic boundary conditions: xyz (default), no (vacuum)
>> ; or full (infinite systems only)
>> ;pbc = no
>> pbc = xyz
>> ; nblist cut-off
>> rlist = 1.0
>> domain-decomposition = no
>>
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> ; Method for doing electrostatics
>> coulombtype = Cut-off  rcoulomb-switch = 0
>> rcoulomb = 1.0
>> ; Dielectric constant (DC) for cut-off or DC of reaction field
>> epsilon-r = 1
>> ; Method for doing Van der Waals
>> vdw-type = User
>> ; cut-off lengths
>> rvdw-switch = 0
>> rvdw = 1.0
>> ; Apply long range dispersion corrections for Energy and Pressure
>> DispCorr = EnerPres
>> ; Extension of the potential lookup tables beyond the cut-off
>> table-extension = 1
>> ; Spacing for the PME/PPPM FFT grid
>> fourierspacing = 0.12
>> ; FFT grid size, when a value is 0 fourierspacing will be used
>> fourier_nx = 0
>> fourier_ny = 0
>> fourier_nz = 0
>> ; EWALD/PME/PPPM parameters
>> pme_order = 4
>> ewald_rtol = 1e-05
>> ewald_geometry = 3d
>> epsilon_surface = 0
>> optimize_fft = no
>>
>> ; GENERALIZED BORN ELECTROSTATICS
>> ; Algorithm for calculating Born radii
>> gb_algorithm = Still
>> ; Frequency of calculating the Born radii inside rlist
>> nstgbradii = 1
>> ; Cutoff for Born radii calculation; the contribution from atoms
>> ; between rlist and rgbradii is updated every nstlist steps
>> rgbradii = 2
>> ; Salt concentration in M for Generalized Born models
>> gb_saltconc = 0
>>
>> ; IMPLICIT SOLVENT (for use with Generalized Born electrostatics)
>> implicit_solvent = No
>>
>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>> ; Temperature coupling
>> ;Tcoupl = yes
>> Tcoupl = Berendsen
>> ; Groups to couple separately
>> tc-grps = System
>> ; Time constant (ps) and reference temperature (K)
>> tau_t = 0.01
>> ref_t = 300
>> ; Pressure coupling
>> ;Pcoupl = Berendsen
>> Pcoupl = no
>> ;Pcoupltype = isotropic
>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
>> tau_p = 5.0
>> compressibility = 4.5e-5
>> ref_p = 1.0
>> ; Random seed for Andersen thermostat
>> andersen_seed = 815131
>>
>> ; SIMULATED ANNEALING
>> ; Type of annealing for each temperature group (no/single/periodic)
>> annealing = no
>> ; Number of time points to use for specifying annealing in each group
>> annealing_npoints =
>> ; List of times at the annealing points for each group
>> ANnealing_time =
>> ; Temp. at each annealing point, for each group.
>> annealing_temp =
>>
>> ; GENERATE VELOCITIES FOR STARTUP RUN
>> gen_vel = yes
>> gen_temp = 300
>> gen_seed = 1993
>>
>> ; OPTIONS FOR BONDS
>> constraints = none
>> ;constraints = all-bonds
>> ; Type of constraint algorithm
>> constraint-algorithm = Lincs
>> ; Do not constrain the start configuration
>> unconstrained-start = no
>> ; Use successive overrelaxation to reduce the number of shake iterations
>> Shake-SOR = no
>> ; Relative tolerance of shake
>> shake-tol = 1e-04
>> ; Highest order in the expansion of the constraint coupling matrix
>> lincs-order = 4
>> ; Number of iterations in the final step of LINCS. 1 is fine for
>> ; normal simulations, but use 2 to conserve energy in NVE runs.
>> ; For energy minimization with constraints it should be 4 to 8.
>> lincs-iter = 1
>> ; Lincs will write a warning to the stderr if in one step a bond
>> ; rotates over more degrees than
>> lincs-warnangle = 30
>> ; Convert harmonic bonds to morse potentials
>> morse = no
>>
>> ; ENERGY GROUP EXCLUSIONS
>> ; Pairs of energy groups for which all non-bonded interactions are
>> excluded
>> energygrp_excl =
>>
>> ; NMR refinement stuff
>> ; Distance restraints type: No, Simple or Ensemble
>> disre = No
>> ; Force weighting of pairs in one distance restraint: Conservative or
>> Equal
>> disre-weighting = Conservative
>> ; Use sqrt of the time averaged times the instantaneous violation
>> disre-mixed = no
>> disre-fc = 1000
>> disre-tau = 0
>> ; Output frequency for pair distances to energy file
>> nstdisreout = 100
>> ; Orientation restraints: No or Yes
>> orire = no
>> ; Orientation restraints force constant and tau for time averaging
>> orire-fc = 0
>> orire-tau = 0
>> orire-fitgrp =
>> ; Output frequency for trace(SD) to energy file
>> nstorireout = 100
>> ; Dihedral angle restraints: No, Simple or Ensemble
>> dihre = No
>> dihre-fc = 1000
>> dihre-tau = 0
>> ; Output frequency for dihedral values to energy file
>> nstdihreout = 100
>>
>> ; Free energy control stuff
>> free-energy = no
>> init-lambda = 0
>> delta-lambda = 0
>> sc-alpha = 0
>> sc-sigma = 0.3
>>
>> ; Non-equilibrium MD stuff
>> acc-grps =
>> accelerate =
>> freezegrps =
>> freezedim =
>> cos-acceleration = 0
>>
>> ; Electric fields
>> ; Format is number of terms (int) and for all terms an amplitude (real)
>> ; and a phase angle (real)
>> E-x =
>> E-xt =
>> E-y =
>> E-yt =
>> E-z =
>> E-zt =
>>
>> ; User defined thingies
>> user1-grps =
>> user2-grps =
>> userint1 = 0
>> userint2 = 0
>> userint3 = 0
>> userint4 = 0
>> userreal1 = 0
>> userreal2 = 0
>> userreal3 = 0
>> userreal4 = 0
>>
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
Ok, Thank you very much, I will wait you reply.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080805/5664b3ff/attachment.html>