Hey, Greg - I believe the problem is more probably located in your GRO file or TOP file rather than in MDP one. Just visualize your structure to check if everything is OK. Also, 50 000 steps can be not enough to get the well-equilibrated configuration. What force and energy is output at the last step of your EM run?
Best of luck. Dr. Vitaly V. Chaban Rochester, U.S.A. > > Has anyone else experienced a pathologically expanding box during > equilibration in the NPT ensemble? I've solvated my system with > editconf/genbox, energy minimized, equilibrated in NVT with the protein > coordinates restrained, and then equilibrated in NPT without any > position restraints. During the NPT equilibration all the box > dimensions are doubling and the density decreases drastically. > > I'm using the v-rescale thermostat and the Berendsen barostat in gromacs > 4.5.3 with the AMBER03 force field and tip3p water. I've also tried > OPLSAA with SPC water, a number of different box types (cubic, > octahedral, dodecahedral), and shorter tau_t and tau_p settings. I also > tried adding another energy minimzation step between my NVT and NPT phases. > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
