Cun Zhang wrote:
hi, Justin. Thank you for your patience !
I'm still in trouble with infinite CNT simulation.
I'm trying to simulate the interaction of a infinite (16,0) CNT(CNT_A)
with 832 atoms and water. I'm using x2top to generate the CNT.itp with
share-bonds. The idea is that I generate a (16,0) CNT(CNT_B) with 960
atoms ( more 4 layer than CNT_A. Each layer has 32 atoms ).
When I use CNT.itp generated by CNT_A and x2top, it works. But when I
use the CNT.itp which has share-bonds information, it can't work.
The process I'm doing CNT simulation is as follows:
# the CNT_new.pdb is a (16,0) CNT with 960 atoms.
# I add the custom forcefield parameters to tmp.top, and change the
number of a charge group to 32, then rename it CNT.itp at the end.
x2top -f CNT_new.pdb -o tmp.top -ff gmx -nopbc -nopairs -noparam -name
CNT
bash sharebond_script # create share bonds
The script below is renumbering and removing atoms. Why are you doing this? I
thought the purpose of CNT_new was to generate a larger structure?
editconf -f CNT.pdb -o -box 3.8 3.8 5.614
Now you are manipulating CNT.pdb - is this the correct next step? If this
actually pertains to CNT_new.pdb, then the box size is insufficient to hold the
larger structure. But now I'm just confused as to what you're doing.
genbox -cp out -cs -p CNT -o b4em.pdb #The simulation box size can be
seen in b4em.pdb
pymol b4em.pdb #remove water. After editing it,I save it as b4em.pdb
too.Now the information about box size is losing. I don't know why.I'm
not familar with it :)
editconf -f b4em.pdb -o b4em -box 3.8 3.8 5.614 # Add the information
about box size
vim CNT.top #change the number of water to make it the same as b4em.pdb
grompp -f em -o em -c b4em -p CNT -maxwarn 5
mpirun -np 4 mdrun_mpi -v -s em -e em -o em -c after_em
Does energy minimization work? What did the potential energy and maximum force
converge to? Again, what is the purpose of "-maxwarn 5"? Are there errors that
grompp is generating that you are simply trying to bypass? This is generally a
bad idea.
-Justin
grompp -f grompp -o pr -c after_em -p CNT -maxwarn 5
mpirun -np 4 mdrun_mpi -v -s pr -e pr -o pr -c after_pr
The sharebond_scrip code:
#!/bin/bash
sed -e '/^ *83[3-9].*UNK/d' -e '/^ *8[4-9][0-9].*UNK/d' -e '/^
*9[0-9][0-9].*UNK/d' CNT.itp >tmp # remove the atoms whose number is
larger than 832 in [ atoms ].
for((i=833;i<=960;i=i+1)) # change the number(i) of atoms which is
larger than 832 to i-832.
do
j=$((i-832))
N=$((3-${#j}))
L=' '
j=${L:1:N}$j
sed -i "s/ $i / $j /" tmp
done
awk '!a[$0]++' tmp>CNT.itp # make the CNT.itp file have no repetitive rows
I upload a log file for more information in there (
http://4message.net/blog/wp-content/uploads/2009/11/CNT.tar.bz2 )
--
========================================
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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