[gmx-users] Justin biphasic tutorial with controlled adsoption of protein

Justin Lemkul jalemkul at vt.edu
Sat May 2 18:23:41 CEST 2015

On 5/2/15 10:02 AM, James Lord wrote:
> Dear gmx users,
> I have a biphasic system, like Justin's tutorial, but I want to control
> the protein to adsorb/desorb from the oil-water interface, I don't want the
> protein to go through oil phase just want to keep it at the interface, I
> have added a constant force at the end of the mdp file. i tried different
> pull_k1 values but what I see is, when the force is applied the oil is also
> deformed (which makes sense) and kinda make a hole in the oil phase and
> eventually pass through it. I just want to keep it at or away from the
> interface without deforming/puling away the oil molecules, What is the best
> way to do it? any suggestion? here is the mdp
> https://drive.google.com/open?id=0B0YMTXH1gmQsZ1ljOUZROWNGM3M&authuser=0

I wouldn't use the pull code.  This sounds like a task best suited for a 
flat-bottom restraint.  I'm going to assume the long axis of the box is along z 
for this example. You can create a coordinate file in which the z-coordinate of 
all the protein atoms is equal to the middle of the box (this assumes the z 
dimension of the box doesn't change, e.g. semiisotropic pressure coupling with 
compressibility of zero along z).  Then supply this file to grompp -r with a 
suitable [position_restraints] section that specifies a flat-bottom potential 
along z (see manual section 4.3.2, I think this is a case where you need a 
negative force constant to keep the atoms "outside" of the restraint region). 
During the run, if any protein atom hits the imaginary wall, it gets pushed back 
in the other direction by the flat-bottom restraint.

Also, don't couple solvent and ions to separate thermostats.  It's not sensible 
and usually not stable.



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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