[gmx-developers] Wall interaction with tabulated potential

Wed Feb 10 14:11:53 CET 2016

Hi,

No! I am not getting the same result. When I used wall-type = 12 -6, I got 16148 kJ/mol and when I used wall-type = table, I got 1344 kJ/mol.

I copied the table 12-6 from the gromacs top directory. I haven't changed anything except wall-type and comb-rule in the topol.top file. (For 12-6 I used 2 and for table I used 1).

Thanks.

Sicnerely,

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: 10 February 2016 13:35
To: gmx-developers at gromacs.org
Subject: Re: [gmx-developers] Wall interaction with tabulated potential

Hi,

I don't understand what you mean with "A" and "C".
If you copy the table from the Gromacs top directory and change the wall-type, but don't change anything elase, you should get the same result as with 12-6.

Cheers,

Berk

On 2016-02-08 14:37, Sudharsan Pandiyan wrote:
Hi,

I tried with sigma =1 and epsilon = 0.25 as well for single particle but no success yet.

Case 1.

I put a particle at 0.5 Angstroms from the surface and calculated potential energy for wall-type=12-6 with sigma = 1 and epsilon = 1.

The potential energy is 16128 kJ/mol

Case 2.

I copied the table 6-12 from the GROMACS top directory as table_A_wall0.xvg and did the same calculation this time with wall-type = table option with A (4*epsilon*sigma^12) and C ( 4*epsilon*sigma^6) values set as 4 .

The potential energy is 1344 kJ/mol

Case 3.

I copied the table 6-12 from the GROMACS top directory as table_A_wall0.xvg and did the same calculation this time with wall-type = table option  with A (4*epsilon/4*sigma^12) and C ( 4*epsilon/4*sigma^6) values set as 1.

The potential energy is 336 KJ/mol.

In table 6-12 from the GROMACS top directory for r value of 0.5 we have the following values,

r    1/r  1/r**2  -1/r**6  -6/r**7  1/r**12   12/r**13

5.0000000000e-01   2.0000000000e+00 4.0000000000e+00   -6.4000000000e+01 -7.6800000000e+02   4.0960000000e+03 9.8304000000e+04

so if i take the value of 4*epsilon*((sigma/r^12)-(sigma/r^6) = 4*1*(4096-64)=16128 kJ/mol. This is what I get when I use wall-type = 12-6, but when I use wall-type = table the results are different.

PS: I also created tables manually and tried both case 2 and 3. The results are same.

Sorry once again for long email.

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 16:01
To: gmx-developers at gromacs.org<mailto:gmx-developers at gromacs.org>
Subject: Re: [gmx-developers] Wall interaction with tabulated potential

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<mailto: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 <mailto:sudharsan.pandiyan at chem.kuleuven.be> <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> [<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 [<mailto:sudharsan.pandiyan at chem.kuleuven.be>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> [<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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