[gmx-users] nve run of carbon nanotube
Adwait Mevada
adwait at imsc.res.in
Tue Nov 16 13:10:11 CET 2010
Dear Gmx-users,
I am simulating a carbon nanotube in vaccum (NVE ensemble). I have taken
parameters of carbon nanotube from "Strong correlations and Fickian
water water
diffusion in narrow carbon nanotube, Biswaroop Mukherjee, Prabal K.
Maiti Chandan
Dasgupta and A. K. Sood, JCP, 126 124704 (2007)".
During the run my carbon nanotube does not remain cylindrical, it
bends inwards and forms
a dumbell shaped structure, also it rotates in space and does not
remain fixed.
My questions are
1) are my itp and mdp parameters correct
2) how do i determine if system is really in ground state or stable
3) temprature keeps on rising as the simulation proceeds is this all right?
----carbon.itp--------
[ defaults ]
1 1
[ atomtypes ]
; name mass charge ptype c6 c12
C 12.0 0.000 A 0.2223431E-02 0.3435E-05
[ nonbond_params ]
;i j funda c6 c12
; self terms
C C 1 0.2223431E-02 0.3435E-05
------cnt.itp----------
[moleculetype ]
;name nrexcl
CNT 3
[ atoms ]
;nr type resnr residue atom cgnr charge
1 C 1 CNT C 1 0.0
2 C 1 CNT C 2 0.0
3 C 1 CNT C 3 0.0
4 C 1 CNT C 4 0.0
5 C 1 CNT C 5 0.0
6 C 1 CNT C 6 0.0
7 C 1 CNT C 7 0.0
8 C 1 CNT C 8 0.0
9 C 1 CNT C 9 0.0
10 C 1 CNT C 10 0.0
11 C 1 CNT C 11 0.0
....
66 C 1 CNT C 66 0.0
67 C 1 CNT C 67 0.0
68 C 1 CNT C 68 0.0
69 C 1 CNT C 69 0.0
70 C 1 CNT C 70 0.0
71 C 1 CNT C 71 0.0
72 C 1 CNT C 72 0.0
[ bonds ]
;harmonic bond parameter Kb = 938 kcal/(molA^2) bo= 1.4 A funct = 1
;harmonic bond parameter Kb = 392459.2 kJ/(mol nm^2) bo= 0.14 nm
;ai aj funct bo kb
1 2 1 0.1400 392459.200
1 24 1 0.1400 392459.200
2 3 1 0.1400 392459.200
3 4 1 0.1400 392459.200
3 26 1 0.1400 392459.200
4 5 1 0.1400 392459.200
4 29 1 0.1400 392459.200
5 6 1 0.1400 392459.200
...
60 61 1 0.1400 392459.200
61 62 1 0.1400 392459.200
62 63 1 0.1400 392459.200
63 64 1 0.1400 392459.200
64 65 1 0.1400 392459.200
65 66 1 0.1400 392459.200
66 67 1 0.1400 392459.200
67 68 1 0.1400 392459.200
68 69 1 0.1400 392459.200
69 70 1 0.1400 392459.200
70 71 1 0.1400 392459.200
71 72 1 0.1400 392459.200
[ angles ]
;harmonic angle funt=1 kth=K0=126 kcal/molrad^2 th0=0c= 2*pi/3 rad
;harmonic angle funt=1 kth=K0=527.184 kJ/molrad^2 th0=0c=120 degrees
;ai aj ak funct th0 kth
1 2 3 1 120.00 527.184
1 24 23 1 120.00 527.184
1 24 25 1 120.00 527.184
2 1 24 1 120.00 527.184
2 3 4 1 120.00 527.184
2 3 26 1 120.00 527.184
3 4 5 1 120.00 527.184
3 4 29 1 120.00 527.184
3 26 25 1 120.00 527.184
3 26 27 1 120.00 527.184
4 3 26 1 120.00 527.184
4 5 6 1 120.00 527.184
4 29 28 1 120.00 527.184
4 29 30 1 120.00 527.184
5 4 29 1 120.00 527.184
5 6 7 1 120.00 527.184
6 7 8 1 120.00 527.184
6 7 30 1 120.00 527.184
7 8 9 1 120.00 527.184
7 8 33 1 120.00 527.184
7 30 29 1 120.00 527.184
7 30 31 1 120.00 527.184
8 7 30 1 120.00 527.184
8 9 10 1 120.00 527.184
8 33 32 1 120.00 527.184
8 33 34 1 120.00 527.184
9 8 33 1 120.00 527.184
9 10 11 1 120.00 527.184
10 11 12 1 120.00 527.184
10 11 34 1 120.00 527.184
11 12 13 1 120.00 527.184
11 12 37 1 120.00 527.184
....
51 52 53 1 120.00 527.184
52 53 54 1 120.00 527.184
53 54 55 1 120.00 527.184
54 55 56 1 120.00 527.184
55 56 57 1 120.00 527.184
56 57 58 1 120.00 527.184
57 58 59 1 120.00 527.184
58 59 60 1 120.00 527.184
59 60 61 1 120.00 527.184
60 61 62 1 120.00 527.184
61 62 63 1 120.00 527.184
62 63 64 1 120.00 527.184
63 64 65 1 120.00 527.184
64 65 66 1 120.00 527.184
65 66 67 1 120.00 527.184
66 67 68 1 120.00 527.184
67 68 69 1 120.00 527.184
68 69 70 1 120.00 527.184
69 70 71 1 120.00 527.184
70 71 72 1 120.00 527.184
-----------cnt.top--------------------
#include "carbon.itp"
#include "cnt.itp"
[ system ]
carbon nanotube in vaccum
[ molecules ]
CNT 1
----------md-vac.mdp----------------------
title = Vaccum MD run ; Title of run
; The following line tell the program the standard locations where to
find certain files
cpp = /lib/cpp ; Preprocessor
; Define can be used to control processes
define = -DFLEXIBLE
; Parameters describing what to do, when to stop and what to save
integrator = md ; Algorithm (steep = steepest
descent minimization)
dt = 0.001
emtol = 1.0 ; Stop minimization when the
maximum force < 1.0 kJ/mol
nsteps = 500000 ; Maximum number of
(minimization) steps to perform
nstenergy = 10 ; Write energies to disk every
nstenergy steps
energygrps = System ; Which energy group(s) to write to disk
; Parameters describing how to find the neighbors of each atom and how
to calculate the
interactions
ns_type = grid ; Method to determine
neighbor list (simple, grid)
coulombtype = cut-off ; Treatment of long range
electrostatic interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
constraints = all-bonds ; Bond types to replace by constraints
pbc = xyz ; Periodic Boundary
Conditions (yes/no)
comm_mode = linear
lincs_iter = 4
lincs_order = 4
Thanks in advance for your help.
-Adwait
Project Assistant,
IMSc, Chennai.
-Adwait
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