[gmx-developers] Wall interaction with tabulated potential

[Berk Hess]

Hi,

I think you didn't understand my answer.
To get the same, your table should contain 1/r^12 and 1/r^6, so you need 
to use sigma=1, epsilon=0.25.

Cheers,

Berk

On 2016-02-05 13:11, Sudharsan Pandiyan wrote:
> Hi,
>
> I tried the tabulated potential with epsilon value 1/4. But still no 
> success.
>
> V(r) = 4*epsilon*((sigma/r)^12-(sigma/r)^6)
>
> sigma = 0.3
> epsilon = 0.4
>
> This is the formula I used to convert my 12-6 potential to a table. I 
> tried both epsilon and epsilon/4 for creating the potential. Later I 
> used this table in csg_call to convert it to a GROMACS table format 
> with 7 columns in which 6th is potential and 7th is force.
>
>
> In this link, 
> <https://www.dropbox.com/s/3vqgvz5ui7mu18r/LJ_WALL.tar.gz?dl=0> I have 
> enclosed a tar ball, which contains 5 folders with 1000 particles 
> under NVT conditions,
>
> 1. BULK system with 12-6 potential : vdwenergy = -156.722
>
> 2. BULK system with tabulated potential : vdwenergy = -157.188
>
> 3. Wall system with 12-6 potential : vdwenergy = -170.088 A-A = 
> -162.01 A-wall0 = -4.14596 A-wall1 = -3.93128
>
> 4. Wall system with Table potential : vdwenergy = -150.295 
> A-A=-161.682 A-wall0 = 5.69261 A-wall1 = 5.69351
>
> 5. Wall system with Table and 1/4 epsilon table potential : vdwenergy 
> = -148.329 A-A=-160.637 A-wall0 = 6.15718 A-wall1 = 6.14995
>
> My problem is with the difference between the A-wall* potentials when 
> comparing 12-6 and tabulated potentials.
>
>
> Sorry for the long email but I desperately need this to continue my work.
>
>
> Sincerely,
>
> Sudharsan
>
>
> ________________________________________
> From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se 
> [gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] on behalf of 
> Berk Hess [hess at kth.se]
> Sent: 05 February 2016 11:22
> To: Discussion list for GROMACS development
> Subject: Re: [gmx-developers] Wall interaction with tabulated potential
>
> Hi,
>
> But epsilon should be 1/4 to match 1/r^12, 1/r^6.
>
> Berk
>
> On Feb 5, 2016 11:17 AM, Sudharsan Pandiyan 
> <sudharsan.pandiyan at chem.kuleuven.be> wrote:
> >
> > Hi,
> >
> > I generated the tables using the csg_call routine from the VOTCA-CSG 
> program and I input 1.0 for sigma and epsilon values in topol.top file 
> (1 also for the combination rule). I also generated the LJ particle 
> interaction table for interaction between the particles in the 
> simulation box, which gives exactly same potential energy for both 
> table potential and 12-6 potential. But the wall-particle interaction 
> produces different values.
> >
> > Sincerely,
> >
> > Sudharsan
> >
> > ________________________________
> > From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se 
> [gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] on behalf of 
> Sudharsan Pandiyan [sudharsan.pandiyan at chem.kuleuven.be]
> > Sent: 05 February 2016 11:08
> > To: gmx-developers at gromacs.org
> > Subject: Re: [gmx-developers] Wall interaction with tabulated potential
> >
> > Hi Berk,
> >
> > Thank you very much for quick reply. But, I input 1.0 for sigma and 
> epsilon values. Still the problem persists.
> >
> > Sincerely,
> >
> > Sudharsan
> > ________________________________
> > From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se 
> [gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] on behalf of 
> Berk Hess [hess at kth.se]
> > Sent: 05 February 2016 10:42
> > To: gmx-developers at gromacs.org
> > Subject: Re: [gmx-developers] Wall interaction with tabulated potential
> >
> > Hi,
> >
> > You should not put sigma and epsilon in the table. The dispersion 
> and repulsion table get multiplied by C6 and C12, respectively.
> >
> > Cheers,
> >
> > Berk
> >
> > On 2016-02-05 09:57, Sudharsan Pandiyan wrote:
> >>
> >> Dear Gmx developers,
> >>
> >> I am trying to simulate a wall option using tabulated potentials 
> option. But it gives different LJ potential values when I compare 12-6 
> potential with the tabulated potential (where the table was generated 
> using same sigma and epsilon values that were used for 12-6 potential).
> >>
> >> I intend to modify my table potential later so I wanted to make 
> sure that it produces correct result. But my test shows that there is 
> a difference between 12-6 and tabulated potentials for wall 
> interaction. Could you please explain what is the difference and how 
> can I get the correct potential energy for tabulated potentials?
> >>
> >> PS: In the manual, its written that both 9-3 and 10-4 are 
> integrated over the surface area and 12-6 potential was applied 
> directly with the z-distance. But how the tabulated potential is 
> represented? (section 7.3.20)
> >>
> >>
> >> Thank you very much for your time and support.
> >>
> >> Sincerely,
> >>
> >> Sudharsan
> >>
> >>
> >>
> >
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