[gmx-developers] Wall interaction with tabulated potential

[Mark Abraham]

I don't know, but if you need an answer to your question, then examining
the behaviour of a single particle in a single-point evaluation is the best
path to understanding how to get it right.

Mark

On Fri, Feb 5, 2016 at 1:24 PM Sudharsan Pandiyan <
sudharsan.pandiyan at chem.kuleuven.be> wrote:

> 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> 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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