[gmx-users] an AFM Pulling failed
jackyxh at 163.com
jackyxh at 163.com
Sun Jul 30 09:03:58 CEST 2006
hi, gmx group and all gmx usrs,
I am doing some MD simulations on CNT's (carbon nanotube) mechanical properties with GROMACS.
first of all, thanks very much for all the suggestions before. I finally got a stable CNT structure with those helps.
I am in trouble again. May anyone help me out:
When I pull the tube, all the atoms flies everywhere at the second step. And, it's strange that at the beginning of the "mdrun", GMX said ,
------------------------------------
reading file ndx30.tpr, VERSION 3.3 (single precision)
Reading parameter file pull10.ppa
Groups: top
Reference Group: bot
Using 1 pull groups
Using distance components 0 0 1
starting mdrun 'ICE'
20 steps, 0.0 ps.
Warning: 1-4 interaction between 5 and 6 at distance 1.295 which is larger than
the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
Writing final coordinates.
-----------------------------------------------------
Which parameter in mdp or pull.ppa could lead to that? Is there probably anything wrong with my mdp file or maybe the gro file? How should I fix it?
1. if I want to apply axial stretching (or compression) on the tube, I should use the AFM pulling code. Am I on the right way?
2. should I do PR before running pulling? (I do not think it's necessary, but maybe it is the certain reason?)
3. should I redo EM? but EM gave me the present gro with total potential very low.
( Potential Energy = -5.5786455e+03
Maximum force = 7.5916821e+02 on atom 267
Norm of force = 5.8862563e+03 ) ----------- Is it ok?
best wishes, and looking forward to any suggestions.
Thanks a lot.
Jacky Allon from SCUT
jackyxh at 163.com
Follows is the md.log file and pullout.ppa attached:
----------------------------------md.log (below)
Input Parameters:
integrator = md
nsteps = 20
init_step = 0
ns_type = Grid
nstlist = 1
ndelta = 2
bDomDecomp = FALSE
decomp_dir = 0
nstcomm = 1
comm_mode = Linear
nstcheckpoint = 2
nstlog = 1
nstxout = 1
nstvout = 100
nstfout = 0
nstenergy = 2
nstxtcout = 0
init_t = 0
delta_t = 0.001
xtcprec = 1000
nkx = 0
nky = 0
nkz = 0
pme_order = 4
ewald_rtol = 1e-05
ewald_geometry = 0
epsilon_surface = 0
optimize_fft = FALSE
ePBC = full
bUncStart = FALSE
bShakeSOR = FALSE
etc = Berendsen
epc = No
epctype = Isotropic
tau_p = 1
ref_p (3x3):
ref_p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
ref_p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress (3x3):
compress[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
compress[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
andersen_seed = 815131
rlist = 0.24 ----------------------I have tried 1.0 and 1.2 too,but the result changed just a little
coulombtype = Cut-off
rcoulomb_switch = 0
rcoulomb = 0.24 -----------------------And this too
vdwtype = Cut-off
rvdw_switch = 0
rvdw = 0.24 ----------------------- And this.
epsilon_r = 1
epsilon_rf = 1
tabext = 1
gb_algorithm = Still
nstgbradii = 1
rgbradii = 2
gb_saltconc = 0
implicit_solvent = No
DispCorr = No
fudgeQQ = 1
free_energy = no
init_lambda = 0
sc_alpha = 0
sc_power = 1
sc_sigma = 0.3
delta_lambda = 0
disre_weighting = Conservative
disre_mixed = FALSE
dr_fc = 1000
dr_tau = 0
nstdisreout = 100
orires_fc = 0
orires_tau = 0
nstorireout = 100
dihre-fc = 1000
dihre-tau = 0
nstdihreout = 100
em_stepsize = 0.01
em_tol = 10
niter = 20
fc_stepsize = 0
nstcgsteep = 1000
nbfgscorr = 10
ConstAlg = Lincs
shake_tol = 1e-04
lincs_order = 4
lincs_warnangle = 30
lincs_iter = 1
bd_fric = 0
ld_seed = 1993
cos_accel = 0
deform (3x3):
deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
grpopts:
nrdf: 2067
ref_t: 300
tau_t: 0.1
anneal: No
ann_npoints: 0
acc: 0 0 0
nfreeze: Y Y Y N N N
energygrp_flags[ 0]: 0
efield-x:
n = 0
efield-xt:
n = 0
efield-y:
n = 0
efield-yt:
n = 0
efield-z:
n = 0
efield-zt:
n = 0
bQMMM = FALSE
QMconstraints = 0
QMMMscheme = 0
scalefactor = 1
qm_opts:
ngQM = 0
CPU= 0, lastcg= 699, targetcg= 350, myshift= 0
nsb->shift = 1, nsb->bshift= 0
Neighbor Search Blocks
nsb->nodeid: 0
nsb->nnodes: 1
nsb->cgtotal: 700
nsb->natoms: 700
nsb->shift: 1
nsb->bshift: 0
Nodeid index homenr cgload workload
0 0 700 700 700
Table routines are used for coulomb: FALSE
Table routines are used for vdw: FALSE
Cut-off's: NS: 0.24 Coulomb: 0.24 LJ: 0.24
System total charge: 0.000
Generated table with 500 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 500 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 500 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest, initial mass: 8400
There are: 700 Atoms
Removing pbc first time
Done rmpbc
**************************************************
PULL INFO
**************************************************
RUN TYPE: Afm
REFERENCE TYPE: center of mass of reference group
Looking for group top: found group top: 10 elements. First: 658
---pulled group, one side of the tube
Looking for group bot: found group bot: 10 elements. First: 1
----ref group, the other side of the tube
Initializing pull groups. Inv. mass of group 1: 0.008333
Initial coordinates center of mass: 1.500 1.500 14.243
----box 3 3 20 and length of tube 8.488
Initializing reference group. Inv. mass: 0.000000
Initial coordinates center of mass: 0.000 0.000 0.000
Initial distance of group 1: 5.757
Pull rate: 1.000000e-03 nm/ns. Force constant: 1.680000e+03 kJ/(mol nm)
Pull direction: 0.000 -0.000 -1.000
------Strange? But I set "afm_dir1 = 0.0 0.0 1.0"
Started mdrun on node 0 Sun Jul 30 03:30:54 2006
Initial temperature: 304.385 K
Step Time Lambda
0 0.00000 0.00000
Grid: 25 x 25 x 166 cells
Configuring nonbonded kernels...
Testing AMD 3DNow support... not present.
Testing ia32 SSE support... present.
++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, J. P. M. Postma, A. DiNola and J. R. Haak
Molecular dynamics with coupling to an external bath
J. Chem. Phys. 81 (1984) pp. 3684-3690
-------- -------- --- Thank You --- -------- --------
Large VCM(group rest): 0.04424, 0.00987, 0.01367, ekin-cm: 9.41453e+00
Energies (kJ/mol)
Morse Angle Proper Dih. LJ-14 Coulomb-14
1.23930e+05 2.50185e+02 2.24203e+03 -8.04751e+03 0.00000e+00
LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy
0.00000e+00 0.00000e+00 1.18375e+05 4.63024e+06 4.74861e+06
Temperature Pressure (bar)
5.38835e+05 1.13207e+06
Step Time Lambda
1 0.00100 0.00000
Large VCM(group rest): -0.03441, 0.03032, 11.52306, ekin-cm: 5.57689e+05
Energies (kJ/mol)
Morse Angle Proper Dih. LJ-14 Coulomb-14
1.62589e+08 1.52028e+05 2.77182e+03 1.35415e+05 0.00000e+00
LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy
0.00000e+00 0.00000e+00 1.62880e+08 5.84601e+09 6.00889e+09
Temperature Pressure (bar)
6.80318e+08 3.82511e+08
Step Time Lambda
2 0.00200 0.00000
Large VCM(group rest): -0.00575, 0.01008, 0.12466, ekin-cm: 6.58298e+01
Energies (kJ/mol)
Morse Angle Proper Dih. LJ-14 Coulomb-14
4.93545e+08 1.10614e+06 1.26717e+04 8.64429e+03 0.00000e+00
LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy
7.72732e+09 0.00000e+00 8.22199e+09 1.38166e+17 1.38166e+17
Temperature Pressure (bar)
1.60788e+16 8.49739e+15
Step Time Lambda
3 0.00300 0.00000
Large VCM(group rest): -25.96824, 170.04892, 230.66357, ekin-cm: 3.47746e+08
Energies (kJ/mol)
Morse Angle Proper Dih. LJ-14 Coulomb-14
4.95650e+08 7.87158e+05 1.35144e+04 -4.57799e+01 0.00000e+00
LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy
3.75407e+14 0.00000e+00 3.75408e+14 8.77067e+26 8.77067e+26
Temperature Pressure (bar)
1.02067e+26 5.39409e+25
Step Time Lambda
4 0.00400 0.00000
Energies (kJ/mol)
Morse Angle Proper Dih. LJ-14 Coulomb-14
4.95603e+08 7.18547e+05 1.31598e+04 4.71733e+01 0.00000e+00
LJ (SR) Coulomb (SR) Potential Kinetic En. Total Energy
1.48841e+11 0.00000e+00 1.49337e+11 nan nan
Temperature Pressure (bar)
nan nan
Step Time Lambda
5 0.00500 0.00000
-------------------------------------------------------
Program mdrun, VERSION 3.3
Source code file: nsgrid.c, line: 226
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.
Variable ci has value -2147483648. It should have been within [ 0 .. 103750 ]
Please report this to the mailing list (gmx-users at gromacs.org)
-------------------------------------------------------
"Don't Grumble, Give a Whistle !" (Monty Python)
----------------------------------------md.log (above)
==========================pullout.ppa (below)
;
; File 'pullout.ppa' was generated
; By user: root (0)
; On host: localhost.localdomain
; At date: Sat Jul 22 20:43:49 2006
;
; GENERAL
verbose = no
Skip steps = 1
; Runtype: afm, constraint, umbrella
runtype = afm
; Number of pull groups
ngroups = 1
; Groups to be pulled
group_1 = top
; The group for the reaction force.
reference_group = bot
; Weights for all atoms in each group (default all 1)
weights_1 =
reference_weights =
; Ref. type: com, com_t0, dynamic, dynamic_t0
reftype = com
; Use running average for reflag steps for com calculation
reflag = 1
; Select components for the pull vector. default: Y Y Y
pulldim = N N Y
; DYNAMIC REFERENCE GROUP OPTIONS
; Cylinder radius for dynamic reaction force groups (nm)
r = 0
; Switch from r to rc in case of dynamic reaction force
rc = 0
; Update frequency for dynamic reference groups (steps)
update = 1
; CONSTRAINT RUN OPTIONS
; Direction, default: 0 0 0, no direction
constraint_direction = 0.0 0.0 0.0
; Constraint distance (nm), default: 0, use starting distance
constraint_distance1 = 0
; Rate of chance of the constraint length, in nm/ps
constraint_rate1 = 0
; Tolerance of constraints, in nm
constraint_tolerance = 1e-06
; AFM OPTIONS
; Pull rates in nm/ps
afm_rate1 = 0.001
; Force constants in kJ/(mol*nm^2)
afm_k1 = 1680
; Directions
afm_dir1 = 0.0 0.0 1.0
; Initial spring positions
afm_init1 = 0 0 8.488
; UMBRELLA SAMPLING OPTIONS
; Force constants for umbrella sampling in kJ/(mol*nm^2)
; Centers of umbrella potentials with respect to reference:
; Ref - Pull.
K1 = 0
Pos1 = 0.0 0.0 0.0
=================================pullout.ppa (above)
--
If you send me one, I will always Re you three, friendship, help or anything else except emails and money:) ――Jacky Allon
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060730/1b9847e9/attachment.html>
More information about the gromacs.org_gmx-users
mailing list