If there's a problem, trjconv can handle it with the use of the right index groups, as suggested at http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions. But it can't keep "these three things" together if there's no index group that describes "these three things." You may need to generate it with make_ndx.
Mark On Thu, Feb 13, 2014 at 11:36 AM, SEMRAN İPEK <semrani...@gmail.com> wrote: > Hi all, > > I am aware of that this topic has been discussed for many times. However, I > need your more guidance whether I am experiencing PBC problem after MD or > not. > My MD box has enzyme+ligand+coenzyme complex. As I have already wrote to > the user list, I am using the force field parameters from literature for > the ligand. And other paramaters related to MD has been checked twice. > After MD what I have seen is that ligand is getting far away from the > active site of the coenzyme. > Justin has mentioned that this is the PBC problem (thank you Justin for > your endless and comprehensive support.). Whatever I do was useless to cure > the PBC problem. > Could you please check my distance file showing the distance between ligand > and coenzyme during MD simulation? > And could you please share your experince if this is the PBC problem or > not?if yes, why trjconvc can not handle it? > > > Best Regards, > > --ipek > > -- > 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.