Justin, thanks for your reply. By the way, your GMX tutorials is great!
I post the gro file and mdp file at the end.
On Thu, Nov 19, 2009 at 10:09 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
>
> Not possible, Gromacs 4.1 hasn't been released :) If you're using version
> 4.0.1, you shouldn't, because it has a nasty bug that affects performance
> very severely.
I'm using GMX 4.0.5, not 4.1. Sorry! :)
> I set the box size larger than CNT's length a C-C bond(half up and half
>> down).
>> If I don't do a EM, it will crumble. But if I do it,it can't satisfy that
>> the box size is larger then CN't length a C-C bond.
>>
>
> I don't understand this. Are you getting any error messages? Screen and
> log output are more useful in most cases.
>
I mean, I make the distance of the top ( or bottom ) C atoms in CNT and the
corresponding edge of the box equals the length of a C-C bond( about 0.142nm
).
I use a (16,0) CNT with 832 atoms ( length 5.472nm).I use the following
command to produce a CNT-water system
>editconf -f CNT.pdb -o -box 3.8 3.8 5.614
No velocities found
system size : 1.270 1.270 5.472 (nm)
center : -0.000 0.000 2.736 (nm)
box vectors : 0.000 0.000 0.000 (nm)
box angles : 0.00 0.00 0.00 (degrees)
box volume : 0.00 (nm^3)
shift : 1.900 1.900 0.071 (nm)
new center : 1.900 1.900 2.807 (nm)
new box vectors : 3.800 3.800 5.614 (nm)
new box angles : 90.00 90.00 90.00 (degrees)
new box volume : 81.07 (nm^3)
>genbox -cp out -cs -p CNT -o b4em.pdb
Output configuration contains 7513 atoms in 2228 residues
Volume : 81.0662 (nm^3)
Density : 1026.51 (g/l)
Number of SOL molecules: 2227
Processing topology
Adding line for 2227 solvent molecules to topology file (CNT.top)
>pymol b4em.pdb # I write a python script to remove the SOL molecules in the
Carbon nanotube.
>editconf -f b4em.pdb -o b4em.gro -box 3.8 3.8 5.614 #rebuild the box.
>grompp -v -f em -c b4em -o em -p CNT -maxwarn 5
NOTE 1 [file CNT.top, line unknown]:
The largest charge group contains 32 atoms.
Since atoms only see each other when the centers of geometry of the charge
groups they belong to are within the cut-off distance, too large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
Checking consistency between energy and charge groups...
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 32x32x48, spacing 0.119 0.119 0.117
Estimate for the relative computational load of the PME mesh part: 0.41
This run will generate roughly 15 Mb of data
writing run input file...
There was 1 note
Back Off! I just backed up em.tpr to ./#em.tpr.1#
gcq#87: "It's Because Of the Metric System" (Pulp Fiction)
>mdrun -v -s em
Back Off! I just backed up md.log to ./#md.log.1#
Getting Loaded...
Reading file em.tpr, VERSION 4.0.5 (single precision)
Loaded with Money
Back Off! I just backed up traj.trr to ./#traj.trr.1#
Back Off! I just backed up traj.xtc to ./#traj.xtc.1#
Back Off! I just backed up ener.edr to ./#ener.edr.1#
starting mdrun 'CNT in water'
50000 steps, 25.0 ps.
step 0Segmentation fault
THE b4em.gro file is like:
GROtesk MACabre and Sinister
7243
1UNK CX 1 2.508 1.929 0.069
1UNK CX 2 2.496 2.053 0.141
1UNK CX 3 2.460 2.172 0.069
1UNK CX 4 2.401 2.282 0.141
.........................
.........................
1UNK CX 828 1.424 1.480 5.541
1UNK CX 829 1.520 1.401 5.469
1UNK CX 830 1.630 1.342 5.541
1UNK CX 831 1.749 1.306 5.469
1UNK CX 832 1.873 1.294 5.541
2SOL OW 833 0.542 1.304 1.163
2SOL HW1 834 0.449 1.297 1.126
2SOL HW2 835 0.553 1.393 1.207
3SOL OW 836 1.716 0.647 0.854
3SOL HW1 837 1.749 0.741 0.854
3SOL HW2 838 1.767 0.593 0.920
.........................
.........................
2137SOL OW 7238 0.214 2.438 5.002
2137SOL HW1 7239 0.252 2.379 5.074
2137SOL HW2 7240 0.254 2.412 4.914
2138SOL OW 7241 3.736 2.968 4.022
2138SOL HW1 7242 3.835 2.957 4.013
2138SOL HW2 7243 3.696 2.882 4.054
3.80000 3.80000 5.61400
The following is my mdp file:
; VARIOUS PREPROCESSING OPTIONS
title = Yo
cpp = /usr/bin/cpp
include =
define =
; RUN CONTROL PARAMETERS
integrator = md
; Start time and timestep in ps
tinit = 0
dt = 0.0005
nsteps = 50000
; For exact run continuation or redoing part of a run
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
; Temperature, friction coefficient (amu/ps) and random seed
;bd-temp = 300
bd-fric = 0
ld-seed = 1993
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 1000
nstvout = 1000
nstfout = 1000
; Checkpointing helps you continue after crashes
nstcheckpoint = 1000
; Output frequency for energies to log file and energy file
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file
nstxtcout = 1000
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 = xyz
periodic_molecules = yes
; nblist cut-off
rlist = 0.9
;domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
rcoulomb-switch = 0
rcoulomb = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field
epsilon-r = 1
; Method for doing Van der Waals
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 0.95
; 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 = v-rescale
; Groups to couple separately
tc-grps = system
; Time constant (ps) and reference temperature (K)
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = no
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1
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
; 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
> I have searched google and gmx mail list, but still can't solve it .
>>
>> I found that GMX online document about Carbon Nanotube(
>> http://www.gromacs.org/index.php?title=Documentation/How-tos/Carbon_Nanotube
>> )
>> say,
>>
>> Be absolutely sure that the "terminal" carbon atoms are sharing a bond in
>> the topology file.
>>
>> I don't understand it.How should I do?
>>
>>
> Make sure there is a bond in your topology between the appropriate atoms at
> one "edge" of the box to the appropriate atoms at the other "edge" of the
> box.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
--
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