[gmx-developers] Wall interaction with tabulated potential

[Mark Abraham]

Hi,

What does one particle interacting with a wall at different distances look
like? You can compute a single point with that by hand, but 1000 particles
is just a guess.

Mark

On Fri, Feb 5, 2016 at 1:11 PM Sudharsan Pandiyan <
sudharsan.pandiyan at chem.kuleuven.be> 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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