Dear Ivan, Thank you. I also think what you are saying that is right. I will also goes through the article. Thank you for article
I actually run the system with simple Gromos96 5316 FF and amber 03 ff. I dont think it will help me With regards, Rama David On Thu, Oct 30, 2014 at 2:27 PM, Ivan Gladich <iglad...@sissa.it> wrote: > Hi, > to the best of my knowledge, > Molecular Dynamics is not the best way to study system stabilized by Pi-Pi > or Pi-Cataion interaction. > > However,in MD people usually overpolarized C-C and C-H bonds to > increase the quadrupole interactions, and thus, mimic the Pi-Pi interaction > > See > http://pubs.acs.org/doi/pdf/10.1021/jp408977b > or > http://pubs.rsc.org/en/content/articlelanding/2006/ > cp/b610253k#!divAbstract > > In conclusion (and in my opinion), you case use MD but be careful and test > your Force field... > > Ivan > > > On 2014-10-30 05:55, rama david wrote: > >> Dear Friends, >> >> I search the archive to find the answer of my question but I did not get >> satisfied answer so I am putting the question in forum. >> >> One of them is as >> http://comments.gmane.org/gmane.science.biology.gromacs.user/51771 >> >> I want to study the MD simulation of Ligand and Receptor that is stabilize >> by >> Pi-Pi and pi-cation interaction >> >> 1. Is it right to say the Pi-Pi and pi-cation interaction can be studied >> by Molecular dynamics?? >> >> 2. Which force field I have to use ?? >> >> 3. In the analysis tools I found that no direct tools can do this >> directly. >> How to do this analysis >> >> I am looking forward for reply. >> >> With best regards, >> > -- > 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.