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<div class="moz-cite-prefix">Hi,<br>
<br>
I think you didn't understand my answer.<br>
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.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2016-02-05 13:11, Sudharsan Pandiyan wrote:<br>
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<div id="divRpF429197" style="direction: ltr;">Hi,</div>
<div><br>
I tried the tabulated potential with epsilon value 1/4. But
still no success.<br>
<br>
V(r) = 4*epsilon*((sigma/r)^12-(sigma/r)^6)<br>
<br>
sigma = 0.3<br>
epsilon = 0.4<br>
<br>
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.<br>
<br>
<br>
<a moz-do-not-send="true"
href="https://www.dropbox.com/s/3vqgvz5ui7mu18r/LJ_WALL.tar.gz?dl=0"
target="_blank">In this link,</a> I have enclosed a tar
ball, which contains 5 folders with 1000 particles under NVT
conditions,<br>
<br>
1. BULK system with 12-6 potential : vdwenergy = -156.722<br>
<br>
2. BULK system with tabulated potential : vdwenergy =
-157.188<br>
<br>
3. Wall system with 12-6 potential : vdwenergy = -170.088
A-A = -162.01 A-wall0 = -4.14596 A-wall1 = -3.93128<br>
<br>
4. Wall system with Table potential : vdwenergy = -150.295
A-A=-161.682 A-wall0 = 5.69261 A-wall1 = 5.69351<br>
<br>
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<br>
<br>
My problem is with the difference between the A-wall*
potentials when comparing 12-6 and tabulated potentials.<br>
<br>
<br>
Sorry for the long email but I desperately need this to
continue my work.<br>
<br>
<br>
Sincerely,<br>
<br>
Sudharsan<br>
<br>
<br>
________________________________________<br>
From: <a class="moz-txt-link-abbreviated" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>
[<a class="moz-txt-link-abbreviated" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>] on
behalf of Berk Hess [<a class="moz-txt-link-abbreviated" href="mailto:hess@kth.se">hess@kth.se</a>]<br>
Sent: 05 February 2016 11:22<br>
To: Discussion list for GROMACS development<br>
Subject: Re: [gmx-developers] Wall interaction with
tabulated potential<br>
<br>
Hi,<br>
<br>
But epsilon should be 1/4 to match 1/r^12, 1/r^6.<br>
<br>
Berk<br>
<br>
On Feb 5, 2016 11:17 AM, Sudharsan Pandiyan
<a class="moz-txt-link-rfc2396E" href="mailto:sudharsan.pandiyan@chem.kuleuven.be"><sudharsan.pandiyan@chem.kuleuven.be></a> wrote:<br>
><br>
> Hi,<br>
><br>
> 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.<br>
><br>
> Sincerely,<br>
><br>
> Sudharsan<br>
><br>
> ________________________________<br>
> From:
<a class="moz-txt-link-abbreviated" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>
[<a class="moz-txt-link-abbreviated" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>] on
behalf of Sudharsan Pandiyan
[<a class="moz-txt-link-abbreviated" href="mailto:sudharsan.pandiyan@chem.kuleuven.be">sudharsan.pandiyan@chem.kuleuven.be</a>]<br>
> Sent: 05 February 2016 11:08<br>
> To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
> Subject: Re: [gmx-developers] Wall interaction with
tabulated potential<br>
><br>
> Hi Berk,<br>
><br>
> Thank you very much for quick reply. But, I input 1.0
for sigma and epsilon values. Still the problem persists.<br>
><br>
> Sincerely,<br>
><br>
> Sudharsan<br>
> ________________________________<br>
> From:
<a class="moz-txt-link-abbreviated" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>
[<a class="moz-txt-link-abbreviated" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>] on
behalf of Berk Hess [<a class="moz-txt-link-abbreviated" href="mailto:hess@kth.se">hess@kth.se</a>]<br>
> Sent: 05 February 2016 10:42<br>
> To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
> Subject: Re: [gmx-developers] Wall interaction with
tabulated potential<br>
><br>
> Hi,<br>
><br>
> You should not put sigma and epsilon in the table. The
dispersion and repulsion table get multiplied by C6 and C12,
respectively.<br>
><br>
> Cheers,<br>
><br>
> Berk<br>
><br>
> On 2016-02-05 09:57, Sudharsan Pandiyan wrote:<br>
>><br>
>> Dear Gmx developers,<br>
>><br>
>> 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).<br>
>><br>
>> 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?<br>
>><br>
>> 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)<br>
>><br>
>><br>
>> Thank you very much for your time and support.<br>
>><br>
>> Sincerely,<br>
>><br>
>> Sudharsan<br>
>><br>
>><br>
>><br>
><br>
--<br>
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