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 editconf -f CNT.pdb -o -box 3.8 3.8 5.614 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 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 ) Cun Zhang wrote: > > Hi, Justin. > > Thank you for your help! I was intended to reply the third question > > after I retryed the simulation under your advice,but I haven't enough > time > > to do it. It's too late :) > > > > Just now, I do a simulation. All seems ok. I will check it again. > > > > Thank you again! > > > > Cun Zhang > > > > > >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? > > > > > > No.I use pymol to remove all residues which is far from the egdes 0.7A . > > > > > > OK. > > > > > > >editconf -f b4em.pdb -o b4em.gro -box 3.8 3.8 5.614 #rebuild > > the box. > > > > Why are you doing this? > > > > > > The b4em.pdb generated by genbox have no information about box size. So > > I use editconf to generate it. > > > > That is not true. Gromacs can handle a number of coordinate file types, > and box > dimensions are written to the CRYST1 line in the .pdb file. You should > never > have to re-define your box unless you are doing some very advanced > manipulations > (which you are not, in the case of simply solvating a structure). > > > > 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. > > > > > > So what's your suggestion about the number of a charge group? > > > > The note from grompp is quite detailed, and even gives examples of > appropriate > charge group sizes. > > -Justin > > > > > -- > > Blog: http://blog.4message.net > > -- > ======================================== > > 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 > -- Blog: http://blog.4message.net
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