[gmx-users] semi-permeable wall in gromacs

Justin Lemkul jalemkul at vt.edu
Tue Apr 19 15:08:10 CEST 2016

On 4/19/16 9:06 AM, gozde ergin wrote:
> Is refcoord_scaling the issue for also NVT simulation?

No, it only applies when pressure coupling is applied.

> Because Roux and Luo did NVT after equilibrate the system in semiisoptropic NPT.

The information you've provided (based on file names and .mdp files) suggests 
you've done this backwards; your data collection should be in NVT so the problem 
I mentioned shouldn't matter.


>> On 19 Apr 2016, at 14:06, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 4/19/16 6:15 AM, gozde ergin wrote:
>>> This is my posre.itp file;
>>> [ position_restraints ]
>>> ; i  funct   g    r(nm)   k
>>>    1     2    5    2.4     4184
>>>    2     2    5    2.4     4184
>>> My box size is 4.8*4.8*9.6. In the reference.gro file z positions of  all of the ions are set to 4.8 so I have two walls at 4.8+2.4=7.2nm  and 4.8-2.4=2.4nm
>>> This step is working without any problem.
>>> Than I use the command of;
>>> gmx traj -f npt.trr -s npt.tpr -n index.ndx -ox coor.xvg -nox -noy
>>> I extract all ions z-coordinate of the ions.
>>> Than I use the equation in Roux2010 paper in order to estimate the osmotic pressure which is,
>>> <Fwall1> = [k (1/N)sum(N) sum(i)(| zi-zwall1 |) and I apply this equation only the ions who have passed the wall.
>>> <Fwall2> = [k (1/N)sum(N) sum(i)(| zi-zwall2 |)
>>> Fwall = (Fwall1 + Fwall2)/2
>>> P = <Fwall>/Area
>>> However I get *very* different results than Roux2010. Even though our temperature, non-bond settings, system size etc are the same.
>>> Has anyone here done simulations to calculate the osmotic pressure and/or osmotic coefficient?
>>> Any suggestion?
>> You may want to try this in CHARMM or NAMD, where it is quite honestly much easier.  All the specifications in GROMACS are relative to the initial configuration, and then there's refcoord_scaling to deal with, so I'm not 100% sure that this is as straightforward as it seems.  In CHARMM and NAMD, the positions of the walls are set explicitly and it is very straightforward to do these calculations.
>>> Also Roux2010 mentioned that the force of the wall is *half harmonic* , what is the force in gromacs for flat-bottom restraint?
>> It's the same.  This just means there's a harmonic potential at the wall.  The flat-bottom restraint says "apply a restraint potential if z > some value" and since there's a second restraint that applies a force if z < some value, each restraint covers half of a harmonic potential.
>> -Justin


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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