[gmx-users] semi-permeable wall in gromacs

Tue Apr 19 14:06:49 CEST 2016

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

>
>> On 07 Apr 2016, at 21:37, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>> On 4/7/16 12:57 PM, gozde ergin wrote:
>>> Hi Justin,
>>>
>>> I just want to ask how is the r(nm) in posre.itp working?
>>>
>>> I would like to put semi-permeable wall on +/- 2.4 nm in z coordinate of the box.
>>>
>>> When I write 2.4 in the r(nm) property for [position_restraints] in posre.itp, it seems all of the molecules that I apply flat-bottom restraint travel +/- 2.4 nm.
>>
>> This is expected.  The flat-bottom potential is established with respect to the reference coordinates.
>>
>>> But I do not want this, I would like to put a wall or force on +/-2.4 nm in z of the box.
>>> Do you have any advice about this?
>>>
>>
>> If you want walls at given z-values, the z-coordinate of species to which the restraint is applied have to be set to zero.  This coordinate file is passed to grompp -r as the reference point for the potential.
>>
>> -Justin
>>
>>> Thanks in advance.
>>>
>>>
>>>> On 21 Mar 2016, at 18:37, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>> On 3/21/16 1:29 PM, gozde ergin wrote:
>>>>> Ok this was a silly question.
>>>>> In g_energy command 5. one is flat-bottom posres force.
>>>>> Sorry.
>>>>>
>>>>
>>>> The output of g_energy is energy, not force.
>>>>
>>>> But the quantity is simple to calculate.  If you have applied a flat-bottom restraint along z, then you just need the time series of the z-coordinates of the restrained particles.
>>>>
>>>> F = k*(z-z0), where z0 is the position at which the flat-bottom restraint is active.  Since there are two walls, then you need to conditions, for +/- z0 and then the final sum should be divided by 2 before being divided by the area of the semipermeable wall.
>>>>
>>>> -Justin
>>>>
>>>>>> On 21 Mar 2016, at 17:26, gozde ergin <gozdeeergin at gmail.com> wrote:
>>>>>>
>>>>>> Hey Justin,
>>>>>>
>>>>>> I am just wondering in order to estimate the osmotic pressure I need extract the flat-bottom restraint force. (Force/Area = Pressure)
>>>>>> Do you have any idea to how to extract this force?
>>>>>>
>>>>>> Thanks in advance
>>>>>>
>>>>>>
>>>>>>
>>>>>>> On 10 Mar 2016, at 15:58, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On 3/10/16 4:44 AM, gozde ergin wrote:
>>>>>>>> Dear Justin,
>>>>>>>>
>>>>>>>> Thanks for your respond, I assume there is a way to apply this restraint on specific molecules.
>>>>>>>> Because my system is mixed with organic and water and I would like to apply these forces on organic molecules not water?
>>>>>>>>
>>>>>>>
>>>>>>> So apply flat-bottom restraints to whatever the organic molecules are.  It's not something specific to ions.  You set the restraints in the molecule's topology (in its [moleculetype]), construct a reference coordinate file that defines some unphysical coordinates to be used as the center of the restraint, and that's it.  I've described the process in detail before so check the archive.
>>>>>>>
>>>>>>> -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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>>>>>>
>>>>>
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> 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 <mailto:jalemkul at outerbanks.umaryland.edu> <mailto:jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu>> | (410) 706-7441
>>>> http://mackerell.umaryland.edu/~jalemkul <http://mackerell.umaryland.edu/~jalemkul> <http://mackerell.umaryland.edu/~jalemkul <http://mackerell.umaryland.edu/~jalemkul>>
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>>>
>>
>> --
>> ==================================================
>>
>> 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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>> Gromacs Users mailing list
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>

-- 
==================================================

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

==================================================