Cun Zhang wrote:
<snip>
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 ).
OK, that sounds reasonable, but did you define the periodic bonds appropriately?
Your original question was that you did not know how to do that.
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.
Are there any solvent molecules interfering with the cross-boundary bonds?
>editconf -f b4em.pdb -o b4em.gro -box 3.8 3.8 5.614 #rebuild the box.
Why are you doing this?
>grompp -v -f em -c b4em -o em -p CNT -maxwarn 5
Are there warnings you are ignoring by using -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.
Pay attention to this note. A charge group of 32 atoms is huge.
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
OK, so what happens? Does the EM converge, or does the minimization fail?
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
Instant crashing indicates the structure is unstable, and that EM likely wasn't
sufficient.
THE b4em.gro file is like:
There is no useful information in the .gro file, and nothing out of the ordinary
in the .mdp file.
-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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