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

[James Lord]

Hi Justin,
Thanks for the info, your assumption re long axis of the box is correct
(z), here is the .gro file I have for one the oil (decane)-protein (the
protein is in the middle part of the free space above the oil surface). Is
that what you were talking about? I went through manual and could not get
what to do for position restrains, appreciate if you can elaborate further
on it? Thanks for your final point re solvent/ions separate coupling.
https://drive.google.com/file/d/0B0YMTXH1gmQsYmQzRXUtN1ZENmc/view?usp=sharing
Cheers
James


On Sun, May 3, 2015 at 4:23 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
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