[gmx-developers] Wall interaction with tabulated potential

Berk Hess hess at kth.se
Wed Feb 10 13:38:45 CET 2016 

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 
> [gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] on behalf of 
> Berk Hess [hess at kth.se]
> *Sent:* 05 February 2016 16:01
> *To:* 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 
>> [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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>
>
>

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