[gmx-users] resize pre-equilibrated system

Justin Lemkul jalemkul at vt.edu
Fri Jul 13 22:53:09 CEST 2018

On 7/13/18 12:07 PM, Roman Sloutsky wrote:
> 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.

You're definitely going to need re-equilibration. You can probably carve 
out the system you want with gmx select to create a geometry-based index 
group, then gmx trjconv to save only those atoms from an existing frame, 
but there's no point trying to preserve velocities or anything. You're 
now creating a new periodic system with interactions that were not 
previously present, and may have clashes or non-optimal geometries. You 
can save your coordinates as you like, but you should minimize and 
equilibrate as if it were a new system; there's no way to do a 
"continuous" simulation in this case.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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