Hi, As you see in the docs http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-refcoord-scaling there are different reference coordinates chosen on your two fragments. The 2018 series of GROMACS prompts you to choose what those coordinates are with grompp -r, which will probably permit the kind of continuity you seek. The feature was always there, but defaulted to the coordinates of grompp -c. Of course the simulations aren't physical, either way.
Mark On Sun, Aug 12, 2018, 11:16 <kai.ex...@alumni.uni-ulm.de> wrote: > Dear Gromacs Users, > > I'm performing MD simulations (NPT) with position restraints for part > of the system, thereby using the refcoord-scaling=com option in the > mdp-file. After the MD run has finished and I'm restarting the MD by > taking the last frame and simply extending the simulation time, I > obtain the following problem: > When calculating certain properties, such as RMSD, radius of gyration > or solvent accessible surface area for the atoms with position > restraints, I obtain an artificial jump in these quantities when > comparing the two subsequent MD runs. This jump directly occurs at the > beginning of the second (extended) MD run. > I ascribe this jump to the rescaling of the com, since the center of > masses in the first frame of the second (extended simulation) is > different than the center of mass in the last frame of the first > simulation. I was also translating the center of masses from the first > frame of the second simulation to the last frame of the first > simulation and then recalculating the above-mentioned properties, > however, without success. > Do you know how to solve this problem? Actually, I verified that this > jump is an artefact, since I was running one of the MDs for the double > time and then the jump does not occur. This jump only arises, when I > extend the time of a MD simulation. > I would be thankful for any help and reply, > Kai > > -- > 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.
