Manik Mayur wrote:
2009/9/8 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
Jennifer Williams wrote:
Hi users,
I am running a very simple simulation of methane inside a pore
(v.much like a carbon nanotube but in my case the tube is
supposed to represent silica.) I keep this tube frozen.
I start with an energy minimisation-however this runs to
completion almost instantly and I keep get NaN for my potential
energy:
Steepest Descents converged to machine precision in 18 steps,
but did not reach the requested Fmax < 10.
Potential Energy = nan
Maximum force = 6.5738518e+01 on atom 2133
Norm of force = 1.5461593e+00
This nan suggests some kind of severe atomic overlap. Reconsider
your coordinates and the box size implied by your coordinate file.
Mark
Otherwise the trajectory looks OK (methane moving around inside
the cylinder). If I go on to use the conf.gro file for an mdrun,
it runs to completion and generates what looks like a reasonable
trajectory, however the output again contains NaN i.e:
Energies (kJ/mol)
LJ (SR) Coulomb (SR) Potential Kinetic En.
Total Energy
nan 0.00000e+00 nan 3.36749e+01
nan
Conserved En. Temperature Pressure (bar)
nan 3.00010e+02 nan
and calculating the Diffusion coefficient gives:
D[ CH4] 613.6682 (+/- 97.0563) 1e-5 cm^2/s
If I do the same calculation but reduce the cut-offs to 0.9. I get
Energies (kJ/mol)
LJ (SR) Coulomb (SR) Potential Kinetic En.
Total Energy
nan 0.00000e+00 nan 3.36750e+01
nan
Conserved En. Temperature Pressure (bar)
nan 3.00011e+02 nan
D[ CH4] 237.8712 (+/- 53.5975) 1e-5 cm^2/s
And for a cut-off of 1.3nm I get
Energies (kJ/mol)
LJ (SR) Coulomb (SR) Potential Kinetic En.
Total Energ
y
nan 0.00000e+00 nan 3.36737e+01
na
n
Conserved En. Temperature Pressure (bar)
nan 2.99999e+02 nan
D[ CH4] 19.7953 (+/- 154.0168) 1e-5 cm^2/s
For this system, the cut-off shouldn?t need to be larger than
0.8 (I have plotted graphs of calculated V vs r) so it is
worrying that the diffusion coefficient is showing such
dependence on the cut-offs when they should all give the same
result.
Can anyone offer any insight into this? I?ve tried changing the
timestep making it both larger and smaller and many other
things. I?ve pasted the relevant parts of my files below:
I?m using gromacs 4.0.5 ?at the moment running in serial.
Thanks for any advice,
Top file
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.0 1.0
;
;
[ atomtypes ]
; type mass charge ptype c6 c12
OSM 15.9994 0.00 A 0.2708 1.538176
Check your tpr file: are the C6 and C12 reasonable?
If you get NaN something is wrong.
;
; Include forcefield parameters
#include "CH4.itp"
;
;
[ moleculetype ]
; Name nrexcl
MCM 3
[ atoms ]
; nr type resnr residue atom cgnr charge
mass
1 OSM 1 MCM OSM 1 0 15.9994
2 OSM 1 MCM OSM 2 0 15.9994
.etc
2127 OSM 1 MCM OSM 2127 0 15.9994
2128 OSM 1 MCM OSM 2128 0 15.9994
[ system ]
; Name
CH4 in MCM
[ molecules ]
; Compound #mols
MCM 1
CH4 10
CH4.itp file
[ atomtypes ]
; type mass charge ptype c6 c12
CH4 16.043 0.00 A 0.3732 1.24650457
;
[ moleculetype ]
; name nrexcl
CH4 2
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 CH4 1 CH4 CH4 1 0.00 16.043
.mdp file
;
; File 'mdout.mdp' was generated
; By user: jwillia4 (353773)
; On host: vlxhead2
; At date: Fri Jun 26 15:47:37 2009
;
; VARIOUS PREPROCESSING OPTIONS
; Preprocessor information: use cpp syntax.
; e.g.: -I/home/joe/doe -I/home/mary/hoe
include = -I../top
; e.g.: -DI_Want_Cookies -DMe_Too
define =
; RUN CONTROL PARAMETERS
integrator = steep
; Start time and timestep in ps
tinit = 0
dt = 0.0001
dt = 0.1 fs are you sure??
nsteps = 100000
; For exact run continuation or redoing part of a run
; Part index is updated automatically on checkpointing (keeps
files separate)
simulation_part = 1
init_step = 0
; mode for center of mass motion removal
comm-mode = linear
; number of steps for center of mass motion removal
nstcomm = 1
; group(s) for center of mass motion removal
comm-grps =
; LANGEVIN DYNAMICS OPTIONS
; Friction coefficient (amu/ps) and random seed
bd-fric = 0
ld-seed = 1993
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol =
emstep = 0.001
; Max number of iterations in relax_shells
niter =
; Step size (ps^2) for minimization of flexible constraints
fcstep =
; Frequency of steepest descents steps when doing CG
nstcgsteep =
nbfgscorr =
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 100
nstvout = 100
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 100
nstenergy = 100
; Output frequency and precision for xtc file
nstxtcout = 100
xtc-precision = 100
; 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 =
; ns algorithm (simple or grid)
ns_type = grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = yes
; nblist cut-off
rlist = 1.7
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Cut-off
rcoulomb-switch = 0
rcoulomb = 1.7
; Relative dielectric constant for the medium and the reaction field
epsilon_r =
epsilon_rf =
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 1.7
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension =
; Seperate tables between energy group pairs
energygrp_table =
; 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 =
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; IMPLICIT SOLVENT ALGORITHM
implicit_solvent = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = no
; Groups to couple separately
tc-grps =
; Time constant (ps) and reference temperature (K)
tau_t =
ref_t =
; Pressure coupling
Pcoupl = No
Pcoupltype =
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p =
compressibility =
ref-p =
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = no
; Random seed for Andersen thermostat
andersen_seed =
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = no
gen_temp = 300
gen_seed = 173529
; OPTIONS FOR BONDS
constraints = none
; Type of constraint algorithm
constraint-algorithm = Lincs
; Do not constrain the start configuration
continuation = no
; Use successive overrelaxation to reduce the number of shake
iterations
Shake-SOR = no
; Relative tolerance of shake
shake-tol = 0.0001
; 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 =
; Non-equilibrium MD stuff
acc-grps =
accelerate =
freezegrps = MCM
freezedim = Y Y Y
cos-acceleration = 0
deform =
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Manik Mayur
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
INDIA
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