Dear Rahul, I really don’t think you understand the concept of pbc in molecular simulations. Please read up on the concept in appropriate literature.
Kind regards, Erik ______________________________ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 26 Jan 2017, at 09:25, RAHUL SURESH <drrahulsur...@gmail.com<mailto:drrahulsur...@gmail.com>> wrote: Thank you But if I am extending my simulation with protein outside the box, then there will not be any effect of water molecules right.? On Thu, 26 Jan 2017 at 1:25 PM, <jkrie...@mrc-lmb.cam.ac.uk<mailto:jkrie...@mrc-lmb.cam.ac.uk>> wrote: Hi Rahul, The protein being out of the box is not a problem except for visualisation and some analysis (e.g. RMSD). For continuing the simulation, it is a completely normal consequence of having periodic boundaries and you shouldn't worry about it. You can then fIx the protein for visualisation and analysis separately to running. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions To continue the simulation just use mdrun as normal but with the -cpi flag. If you want more time than you originally set the mdp to ask for then use tpbconv (gmx convert_tpr in gromacs 5 and later). See http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Best wishes James Hi mark I want to extend it for another 50ns. At 100ns protein is out of the box. Now is t possible to apply boundary conditions and extend.? On Wed, 25 Jan 2017 at 11:12 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: Hi, On Wed, 25 Jan 2017 18:00 RAHUL SURESH <drrahulsur...@gmail.com> wrote: from production output of a monomer for 100ns, there s a instability in the structure from 83ns to 100ns. Many things could be going on here... Also .gro file shows, the protein is out of the cube. Mdrun doesn't care. There's infinitely many equivalent representations of a periodic system. http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions gmx make_ndx -f md.gro -o index.ndx trjconv -f md.xtc -s md.tpr -n index.ndx -pbc mol -ur compact -center -o outputfile.xtc I used the above commands to bring the protein to the center of the box. gmx trjconv -f outputfile.xtc -s md.tpr -o newmd.trr And using the above command, extracted a trr file. Now can I extend this job with this trr file as it is or should i give any periodic boundary conditions or should take the conformer structure at 80ns and run for another 50ns? None of this is needed. See http://www.gromacs.org/Documentation/How-tos/Extending_Simulations Whether it makes sense to try to repeat or extend or go back to the start and try to fix something depends on what the "instability" is, and what is causing it. Mark waiting for your valuable note. -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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. -- 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. -- 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<mailto: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.