ucsd mail wrote: > Hi There, > > I am a new user of Gromacs and want to work on carbon nanotubes. > 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.
You cannot have a bonded interaction between atoms that belong to different [ moleculetype ] directives. So you will need to make a hybrid of the nanotube and the polymer. Depending on what sense you think it will be "better" to have them as separate molecules, you may wish to define index groups with make_ndx for whatever use you have in mind. Mark > Currently my .top file looks like this: (Thanks a lot!) > ******************************************* > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 1 > > [ atomtypes ] > ; type mass charge ptype c6 c12 > C 12.0 0.0 A 0.0 0.0 > X 1.0e10 0.0 A 0.0 0.0 > OW 15.994 -0.82 A 0.0 0.0 > H 1.008 0.41 A 0.0 0.0 > ...more info > > [ nonbond_params ] > ; ai aj funct aij bij > C C 1 2.8768001E-3 4.691598E-6 > OW OW 1 2.6169064E-3 2.633236E-6 > C OW 1 1.3176287E-3 1.388472E-6 > ...more info > > [ bondtypes ] > ; i j func b0 kb beta > C C 3 0.1418 478.9 21.867 > ...more info > > [ angletypes ] > ;i j k func th0 cth > C C C 2 120.0 562.2 > ...more info > > [ dihedraltypes ] > ; i j func phi0 cp mult > C C 1 180.0 12.56 2 > ...more info > > #include "cnt_test.itp" > #include "FLEXSPC.itp" > #include "polymer.itp" > > [ system ] > CNT_H2O > > [ molecules ] > CNT 1 > SOL 1419 > POL 2 > ********************************************* > > 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. > ********************************************* > [ bonds ] > ; ai aj funct b0 kb > 3 4 1 1.000000e-01 3.744680e+05 > 3 5 1 1.000000e-01 3.744680e+05 > 6 7 1 1.000000e-01 3.744680e+05 > 6 8 1 1.000000e-01 3.744680e+05 > 1 2 1 1.230000e-01 5.020800e+05 > 1 3 1 1.330000e-01 3.765600e+05 > 1 6 1 1.330000e-01 3.765600e+05 > ************************************************* > > Regards, > Stone > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
