[gmx-users] resize pre-equilibrated system

Roman Sloutsky sloutsky at umass.edu
Fri Jul 13 18:07:23 CEST 2018

I have been simulating a system of protein in explicit water under PBC. When I first prepared the system for simulation, the protein had an extended flexible linker (it was modeled in). I surrounded it with a water box with some padding past the edge of the extended linker.

During the simulation I’ve already performed the linker collapsed into a globular conformation, and now I have an excess amount of water surrounding the protein. I expect this collapsed configuration to persist for a long time, so I would like to avoid simulating all that bulk water unnecessarily. On the other hand, the system is already equilibrated, and I would rather not re-solvate the new configuration of the protein from scratch.

Is it possible to use gmx tools to re-size the system and remove the excess water molecules, maintaining the position of the protein at the center of the unit box? Maintaining the velocities of the remaining molecules (to avoid any additional equilibration) would be a nice bonus, but equilibrating from the last frame of a well-behaved simulation would still be better than equilibrating a new system.

I do have counter ions, some of which might end up betting excluded and would need to be placed back into the new box. Therefore, some minimal equilibration might still be required.

I would appreciate any help!


|| Roman Sloutsky, PhD   ●   Postdoctoral Research Associate ||
|| Stratton Lab     ●     Biochemistry and Molecular Biology ||
|| University of Massachusetts Amherst ●  sloutsky⏣umass.edu ||

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