On Thu, Feb 12, 2015 at 12:09 AM, Ting Zheng <zhengting...@gmail.com> wrote:
> Hi all, > I have a problem that puzzle me a long time. > In my system I define a angle and two bonds between 2-1-3 and 2-1, 2-3 > atoms. Generally the coulomb and LJ interaction between 1-3, 1-2, 2-3 atoms > was excluded. However, in my position, the potential parameters for these > three atoms is quite abnormal since the interaction (only coulombic > interactions) in 1-3 atoms was still existed which means I have add this > special interaction into my non-bonded list. > So my question is that how should I add this special interactions? I am > using Amber force field. It seems that the [pairs] items in the top file > can make this special interaction come true. But It seems that additional > interaction in 1-4 atom could be added via using the [pairs] items. But I > am not quite about this. Is there anyone who can do me a favor about this > problem? > [pairs] are used to add modified 1-4 interactions, but in principle can be used to add anything, such as 1-3 in your case. > Secondly, how should I use only coulomb interactions in my system? > Set VDW parameters to zero, mdrun will gleefully take advantage of that! Mark > Thanks very much > > Best Regards > Ting > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.