hi, Justin. Thank you for your patience ! <br><br>I'm still in trouble with infinite CNT simulation.<br><br>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 ).<br>
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.<br><br><br>The process I'm doing CNT simulation is as follows:<br><div style="margin-left: 40px;">
# the CNT_new.pdb is a (16,0) CNT with 960 atoms.<br># 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.<br><br></div><div style="margin-left: 40px;">x2top -f CNT_new.pdb -o tmp.top -ff gmx -nopbc -nopairs -noparam -name CNT <br><br>bash sharebond_script # create share bonds<br>
<br>editconf -f CNT.pdb -o -box 3.8 3.8 5.614<br><br>genbox -cp out -cs -p CNT -o b4em.pdb #The simulation box size can be seen in b4em.pdb<br><br>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 :)<br>
<br>editconf -f b4em.pdb -o b4em -box 3.8 3.8 5.614 # Add the information about box size<br>vim CNT.top #change the number of water to make it the same as b4em.pdb<br>grompp -f em -o em -c b4em -p CNT -maxwarn 5<br>mpirun -np 4 mdrun_mpi -v -s em -e em -o em -c after_em<br>
grompp -f grompp -o pr -c after_em -p CNT -maxwarn 5<br>mpirun -np 4 mdrun_mpi -v -s pr -e pr -o pr -c after_pr<br><br></div>The sharebond_scrip code:<br><div style="margin-left: 40px;"><br></div><div style="margin-left: 40px;">
#!/bin/bash<br>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 ].<br>for((i=833;i<=960;i=i+1)) # change the number(i) of atoms which is larger than 832 to i-832.<br>
do<br> j=$((i-832))<br> N=$((3-${#j}))<br> L=' ' <br> j=${L:1:N}$j<br> sed -i "s/ $i / $j /" tmp<br>done<br>awk '!a[$0]++' tmp>CNT.itp # make the CNT.itp file have no repetitive rows<br>
</div><br>I upload a log file for more information in there ( <a href="http://4message.net/blog/wp-content/uploads/2009/11/CNT.tar.bz2">http://4message.net/blog/wp-content/uploads/2009/11/CNT.tar.bz2</a> )<br><br><div class="gmail_quote">
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Cun Zhang wrote:<br>
> Hi, Justin.<br>
> Thank you for your help! I was intended to reply the third question<br>
> after I retryed the simulation under your advice,but I haven't enough time<br>
> to do it. It's too late :)<br>
><br>
> Just now, I do a simulation. All seems ok. I will check it again.<br>
><br>
> Thank you again!<br>
><br>
> Cun Zhang<br>
><br>
> > >pymol b4em.pdb # I write a python script to remove the SOL<br>
> molecules<br>
> > in the Carbon nanotube.<br>
><br>
> Are there any solvent molecules interfering with the cross-boundary<br>
> bonds?<br>
><br>
><br>
> No.I use pymol to remove all residues which is far from the egdes 0.7A .<br>
><br>
><br>
<br>
OK.<br>
<br>
><br>
> > >editconf -f b4em.pdb -o b4em.gro -box 3.8 3.8 5.614 #rebuild<br>
> the box.<br>
><br>
> Why are you doing this?<br>
><br>
><br>
> The b4em.pdb generated by genbox have no information about box size. So<br>
> I use editconf to generate it.<br>
><br>
<br>
That is not true. Gromacs can handle a number of coordinate file types, and box<br>
dimensions are written to the CRYST1 line in the .pdb file. You should never<br>
have to re-define your box unless you are doing some very advanced manipulations<br>
(which you are not, in the case of simply solvating a structure).<br>
<br>
> > NOTE 1 [file CNT.top, line unknown]:<br>
> > The largest charge group contains 32 atoms.<br>
> > Since atoms only see each other when the centers of geometry of<br>
> the charge<br>
> > groups they belong to are within the cut-off distance, too<br>
> large charge<br>
> > groups can lead to serious cut-off artifacts.<br>
> > For efficiency and accuracy, charge group should consist of a<br>
> few atoms.<br>
> > For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2,<br>
> CO, etc.<br>
> ><br>
><br>
> Pay attention to this note. A charge group of 32 atoms is huge.<br>
><br>
><br>
> So what's your suggestion about the number of a charge group?<br>
><br>
<br>
The note from grompp is quite detailed, and even gives examples of appropriate<br>
charge group sizes.<br>
<br>
-Justin<br>
<br>
><br>
> --<br>
> Blog: <a href="http://blog.4message.net/" target="_blank">http://blog.4message.net</a><br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><font color="#888888"><br>
</font></blockquote><br></div><br><br clear="all"><br>-- <br>Blog: <a href="http://blog.4message.net" target="_blank">http://blog.4message.net</a><br>