[gmx-users] Re: pathologically expanding box

[Vitaly Chaban]

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.
>