In molecular dynamics things move around. The fact that the molecules aren't in the starting position shows that it isn't a stable configuration, the interactions between the protein and the molecules are insufficient to keep them together in that spot.
Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Thu, 28 Mar 2019 at 05:50, saranya <saranyahone...@gmail.com> wrote: > Hi users, > > I have simulated a protein with gas molecules (CO2,NO2 and SO2) for > 100ns. I have followed the protein ligand tutorial. I have applied > position constraints. After equilibrium the gas molecules are at the docked > position but at the 60ns simulation the gas molecules are far away from the > protein. I have applied pBC and sure this is not an visualisatuin error. > How can I rectify this, Kindly give your valuable suggestions in this > regard. > > > > -- > > *Saranya Vasudevan,* > > *Research Scholar,* > > *Molecular Quantum Mechanics Laboratory,* > > *Department of Physics,* > > *Bharathiar University,* > > *Coimbatore-46* > -- > 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.