[gmx-users] How to do an osmotic pressure calculation in Gromacs 5.1.4.

Miner, Jacob Carlson jcminer at lanl.gov
Tue Apr 25 16:29:28 CEST 2017


I am trying to set up a cube (LxLxL) of 2000 TIP3P waters and 72 urea molecules at 300 K with an adjacent cube (LxLxL) containing only water.

The aim with this system is to place a semipermeable membrane between along the dimension of the two LxLxL boxes (now a box of LxLx2L) so that a cosolvent particle that attempts to cross from one box to the other (Z displacement < 0 or Z-disp > L) will be pushed back by a flat-bottom potential. The water, meanwhile, should be allowed to transit through the entire 2L Z-dimension without any opposing force. Periodic boundary conditions will be present along the X and Y dimensions as well.

This was accomplished in a previous version of gromacs assembled by my colleagues in gromacs 4.0.7 and 4.5.5 who actually added their own pulling potential to the code.

As the formatting has changed, and now a flat-bottom potential is included in the newer versions of Gromacs, I wanted to know if anyone can explain how the code could be set up to allow this kind of force measurement to be conducted in Gromacs v5.1.4?


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