[gmx-developers] Wall interaction with tabulated potential

Fri Feb 5 13:24:15 CET 2016

Hi,

Yeah! indeed 1000 particles is an example but my question remains same.

Why there is a difference between 12-6 and tabulated potential when I use the same sigma and epsilon to prepare the table?

Thank you for your valuable time and quick reply.

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 Mark Abraham [mark.j.abraham at gmail.com]
Sent: 05 February 2016 13:15
To: gmx-developers at gromacs.org
Subject: Re: [gmx-developers] Wall interaction with tabulated potential

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<mailto: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<mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> [gromacs.org_gmx-developers-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se>] on behalf of Berk Hess [hess at kth.se<mailto: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<mailto: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<mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> [gromacs.org_gmx-developers-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se>] on behalf of Sudharsan Pandiyan [sudharsan.pandiyan at chem.kuleuven.be<mailto:sudharsan.pandiyan at chem.kuleuven.be>]
> Sent: 05 February 2016 11:08
> To: gmx-developers at gromacs.org<mailto: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<mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se> [gromacs.org_gmx-developers-bounces at maillist.sys.kth.se<mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se>] on behalf of Berk Hess [hess at kth.se<mailto:hess at kth.se>]
> Sent: 05 February 2016 10:42
> To: gmx-developers at gromacs.org<mailto: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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