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<DIV><FONT face=Calibri>Hi There,</FONT></DIV>
<DIV><FONT face=Calibri></FONT> </DIV>
<DIV><FONT face=Calibri>I am a new user of Gromacs and want to work on
carbon nanotubes. </FONT></DIV>
<DIV><FONT face=Calibri>I want to simulation carbon nanotube(cnt) bonded with
polymers in water. And it will be much better to consider cnt and the
bonded polymer as separate molecules, instead of one molecule. I
can create the .itp file for both the nanotube and the polymer chain, and
include them in the .top file. But I do not know how to describe the bond betwen
the cnt and the polymer. </FONT></DIV>
<DIV><FONT face=Calibri>Currently my .top file looks like this: (Thanks a
lot!)</FONT></DIV>
<DIV><FONT face=Calibri>*******************************************</FONT></DIV>
<DIV><FONT face=Calibri>[ defaults ]<BR>; nbfunc
comb-rule gen-pairs fudgeLJ
fudgeQQ<BR>
1 1
</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Calibri>[ atomtypes ]<BR>; type
mass charge ptype
c6
c12<BR> C
12.0 0.0
A
0.0
0.0<BR> X
1.0e10 0.0
A
0.0
0.0<BR> OW 15.994
-0.82 A
0.0
0.0<BR> H
1.008 0.41
A
0.0
0.0<BR> ...more info</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Calibri>[ nonbond_params ]<BR>;
ai aj funct
aij
bij<BR> C C
1 2.8768001E-3
4.691598E-6 <BR> OW OW
1 2.6169064E-3
2.633236E-6<BR> C OW
1 1.3176287E-3
1.388472E-6<BR> ...more info</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Calibri>[ bondtypes ]<BR>; i j func
b0 kb beta<BR> C C 3
0.1418 478.9 21.867 <BR> ...more info</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Calibri>[ angletypes ]<BR>;i j k func
th0 cth<BR> C C C 2
120.0 562.2<BR> ...more info</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Calibri>[ dihedraltypes ]<BR>; i
j func phi0
cp mult<BR> C
C 1 180.0
12.56 2<BR> ...more info</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Calibri>#include "cnt_test.itp"<BR>#include
"FLEXSPC.itp"<BR>#include "polymer.itp"</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Calibri>[ system ]<BR>CNT_H2O</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=Calibri>[ molecules ]<BR>CNT 1<BR>SOL
1419<BR>POL 2</FONT></DIV>
<DIV><FONT
face=Calibri>*********************************************</FONT></DIV>
<DIV><FONT face=Calibri></FONT> </DIV>
<DIV><FONT face=Calibri>I read the manual and found an example that include
bonds in topology file like below. The atom IDs are specified instead of atom
type. Can I do this for atom (ID) in different molecules?
Thanks.</FONT></DIV>
<DIV><FONT
face=Calibri>*********************************************</FONT></DIV>
<DIV><FONT face=Calibri>[ bonds ]<BR>; ai aj funct b0 kb<BR>3 4 1 1.000000e-01
3.744680e+05<BR>3 5 1 1.000000e-01 3.744680e+05<BR>6 7 1 1.000000e-01
3.744680e+05<BR>6 8 1 1.000000e-01 3.744680e+05<BR>1 2 1 1.230000e-01
5.020800e+05<BR>1 3 1 1.330000e-01 3.765600e+05<BR>1 6 1 1.330000e-01
3.765600e+05</FONT></DIV>
<DIV><FONT
face=Calibri>*************************************************</FONT></DIV>
<DIV><FONT face=Calibri></FONT> </DIV>
<DIV><FONT face=Calibri>Regards,</FONT></DIV>
<DIV><FONT face=Calibri>Stone</FONT></DIV></BODY></HTML>