[gmx-users] How to do an osmotic pressure calculation in Gromacs 5.1.4.
jalemkul at vt.edu
Tue Apr 25 16:37:41 CEST 2017
On 4/25/17 10:29 AM, Miner, Jacob Carlson wrote:
> 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?
You can do it in 5.1.4 using a series of steps employing flat-bottom
[position_restraints] but it is rather complex. I suggest using the pull code
of version 2016.3:
You'll set two restraints, one with type "flat-bottom" and the other with
"flat-bottom-high" and specify the atoms to which the restraint is applied along
the z-axis. That should be all there is to it (I have not tried this method but
it should work; I have been doing osmotic pressure calculations in NAMD where it
is also very easy).
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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