[gmx-users] semi-permeable wall in gromacs
gozde ergin
gozdeeergin at gmail.com
Tue Apr 19 15:06:03 CEST 2016
Is refcoord_scaling the issue for also NVT simulation?
Because Roux and Luo did NVT after equilibrate the system in semiisoptropic NPT.
> 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
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