[gmx-users] semi-permeable wall in gromacs

[gozde ergin]

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
> 
> -- 
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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