[gmx-users] table force-field

Tue Aug 5 13:50:24 CEST 2008

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

>
>
> Alexandr Malafeev wrote:
>
>> Hi Gromacs Users,
>>
>> In my simulation I have use very complicated potential, I obtained this
>> potential from Boltzman Inversion of rdf, but when I trying run simulation I
>> get error
>>
>> Range checking error:
>> Explanation: During neighborsearching, we assign each particle to a grid
>> based on its coordinates. If your system contains collisions or parameter
>> errors that give particles very high velocities you might end up with some
>> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
>> put these on a grid, so this is usually where we detect those errors.
>> Make sure your system is properly energy-minimized and that the potential
>> energy seems reasonable before trying again.
>>
>> Can you help me?
>>
>
> There are two potential sources of error here.  Either there is something
> wrong with the potential function you're using (i.e., a typo or
> miscalculation) or you have a physically unrealistic system.  Did you do
> energy minimization, and did it converge to an appropriate potential energy,
> as the mdrun output says?
>
> Without knowing more about your system or the run parameters, it is
> difficult to give more details.
>
> -Justin
>
>
>> Thanks in advance.
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> 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

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
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080805/1ce4657f/attachment.html>