Hi, What are you exchanging between replicas? Seems like the most likely issue.
Mark On Sat, 24 Jun 2017 16:50 Qinghua Liao <scorpio.l...@gmail.com> wrote: > Hello, > > I have searched on Google for the LINCS warning problems, and there are > already many discussions, > but I guess that my situation might be different. > > I have a system of protein/micelles/water_ions in a dodecahedral water > box. The system is fully equilibrated by several steps. > > 1. minimizations (steep, cg) with positional restraints (1000 kJ/mol > nm2) on protein and micelles, > 2. 500 ps NVT equilibration, time step 1 fs, positional restraints (1000 > kJ/mol nm2) on protein and micelles, > 3. 500 ps NPT equilibration, time step 1 fs, positional restraints (1000 > kJ/mol nm2) on protein and micelles, > 4. 500 ps NPT equilibration, time step 1 fs, positional restraints (800 > kJ/mol nm2) on protein and micelles, > ...500 ps, restraints, 600 kJ/mol nm2, 1fs > ...500 ps, restraints, 400 kJ/mol nm2, 1fs > ...500 ps restraints, 200 kJ/mol nm2, 1fs > ... 500 ps restraints, 100 kJ/mol nm2, 1 fs > > 5. 15 ns equilibration, positional restraints (100 kJ/mol nm2) only on > protein, letting the micelles assemble, time step 1 fs > 6. 5 ns MD simulation, without any restraints, time step 2 fs > > For all these steps, the constraints were applied to h-bonds, which is > the same for following simulations. > And the I started a Hamiltonian replica exchange simulation, 4 replicas > were chosen, time step is 2fs. > But the simulation crashed at the simulation time of 25 ns. The error is > shown like: > # > step 12855987: Water molecule starting at atom 66929 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > Wrote pdb files with previous and current coordinates > Wrote pdb files with previous and current coordinates > # > Step 12855991, time 25712 (ps) LINCS WARNING in simulation 3 > relative constraint deviation after LINCS: > rms 0.000678, max 0.010615 (between atoms 3541 and 3542) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 3541 3543 90.0 0.1010 0.1020 0.1010 > # > > Atom 3541 is ND2 of ASN227, and atom 3543 is HD22 bonded to atom 3541. I > checked the trajectory file, and I didn't find Asn227 doing something > improperly. > > I also found that the constraints failure happened faster if I used 2 fs > with constraints for all bonds. I believe that a time step of 1 fs will > work, which also means > more computing time since the system is very big. Any suggestions? > Thanks very much! > > > > All the best, > Qinghua > > -- > 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.
