<div dir="ltr">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.<div><br></div><div>Mark</div></div><br><div class="gmail_quote"><div dir="ltr">On Fri, Feb 5, 2016 at 1:24 PM Sudharsan Pandiyan <<a href="mailto:sudharsan.pandiyan@chem.kuleuven.be">sudharsan.pandiyan@chem.kuleuven.be</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">Hi,
<div><br>
</div>
<div>Yeah! indeed 1000 particles is an example but my question remains same. </div>
<div><br>
</div>
<div>Why there is a difference between 12-6 and tabulated potential when I use the same sigma and epsilon to prepare the table? </div>
<div><br>
</div>
<div>Thank you for your valuable time and quick reply.</div>
<div><br>
</div>
<div>Sincerely,</div>
<div><br>
</div>
<div>Sudharsan</div>
<div> <br>
<div style="font-family:Times New Roman;color:#000000;font-size:16px">
<hr>
<div style="direction:ltr"><font face="Tahoma" size="2" color="#000000"><b>From:</b> <a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a> [<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>] on behalf of Mark Abraham [<a href="mailto:mark.j.abraham@gmail.com" target="_blank">mark.j.abraham@gmail.com</a>]<br>
<b>Sent:</b> 05 February 2016 13:15</font></div></div></div></div></div><div><div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt"><div><div style="font-family:Times New Roman;color:#000000;font-size:16px"><div style="direction:ltr"><font face="Tahoma" size="2" color="#000000"><br>
<b>To:</b> <a href="mailto:gmx-developers@gromacs.org" target="_blank">gmx-developers@gromacs.org</a><br>
<b>Subject:</b> Re: [gmx-developers] Wall interaction with tabulated potential<br>
</font></div></div></div></div></div><div><div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt"><div><div style="font-family:Times New Roman;color:#000000;font-size:16px">
<div></div>
<div>
<div dir="ltr">Hi,
<div><br>
</div>
<div>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.
<div><br>
</div>
<div>Mark</div>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr">On Fri, Feb 5, 2016 at 1:11 PM Sudharsan Pandiyan <<a href="mailto:sudharsan.pandiyan@chem.kuleuven.be" target="_blank">sudharsan.pandiyan@chem.kuleuven.be</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">
<div style="font-family:Times New Roman;color:#000000;font-size:16px">
<div 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 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 href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">
gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a> [<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>] on behalf of Berk Hess [<a href="mailto:hess@kth.se" target="_blank">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 href="mailto:sudharsan.pandiyan@chem.kuleuven.be" target="_blank">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 href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">
gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a> [<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>] on behalf of Sudharsan Pandiyan [<a href="mailto:sudharsan.pandiyan@chem.kuleuven.be" target="_blank">sudharsan.pandiyan@chem.kuleuven.be</a>]<br>
> Sent: 05 February 2016 11:08<br>
> To: <a href="mailto:gmx-developers@gromacs.org" target="_blank">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 href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">
gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a> [<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>] on behalf of Berk Hess [<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>]<br>
> Sent: 05 February 2016 10:42<br>
> To: <a href="mailto:gmx-developers@gromacs.org" target="_blank">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>
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