Hi >From Justin: " Yes, as long as those atoms are listed as bonded within the [ bonds ] section of your .top file. "
The specific "bonded function", such as gb_28", should be also listed on the [bonds] section, right? Or, it could assign NOTHING for me, right? so, [bonds] ; ai aj funct 8 9 gb_28 is correct....... [bonds] ; ai aj funct 8 9 is INCORECT....... and 8 , 9 will NOT be automatically bonded, right? The same for the nonbonded parts, right? Thank you Lin On 9/22/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > > Chih-Ying Lin wrote: > > > HI > > > > The command > > #include "ffXXX.itp" is putting in the .top file. > > > > How does this command automatically assign the force field > > parameters which I did not assign in my .top file? > > > > Is it based on the atom types which I assign in my .top file? > > Then, all the force field parameters from "include ffXXX.itp" will > > give the both bonded > > and non-bonded parameters according the atom types, right? > > > > > > I mean...... once I determine the atom type.......such as NL and CH3...... > > there is a bond between NL and CH3..... > > But i did not assign the bond parameters in my .top file while I add > > the command > > "#include "ffXXX.itp" in my .top file. > > > > Will this command #include "ffXXX.itp" automatically assign a bond > > parameter for it? > > > > > > > > Yes, as long as those atoms are listed as bonded within the [ bonds ] > section of your .top file. > > > > > > Other than this, there are so many non-bonded force field parameters. > > Once, I determine the atom types such as O and CR1. > > But, I did not assign any non-bonded parameters for them in my .top file. > > Will this command #include "ffXXX.itp" assign all the non-bonded > > force field parameters for me based on the atom types automatically? > > > > > > Yes. > > -Justin > > > > > > Thank you > > Lin > > > > > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
