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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi,
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>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).</div>
<div><br>
</div>
<div>Thanks.</div>
<div><br>
</div>
<div>Sicnerely,</div>
<div><br>
</div>
<div>Sudharsan</div>
<div><br>
</div>
<div><br>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF411017" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> gromacs.org_gmx-developers-bounces@maillist.sys.kth.se [gromacs.org_gmx-developers-bounces@maillist.sys.kth.se] on behalf of Berk Hess [hess@kth.se]<br>
<b>Sent:</b> 10 February 2016 13:35<br>
<b>To:</b> gmx-developers@gromacs.org<br>
<b>Subject:</b> Re: [gmx-developers] Wall interaction with tabulated potential<br>
</font><br>
</div>
<div></div>
<div>
<div class="moz-cite-prefix">Hi,<br>
<br>
I don't understand what you mean with "A" and "C".<br>
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.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 2016-02-08 14:37, Sudharsan Pandiyan wrote:<br>
</div>
<blockquote type="cite">
<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hi,
<div><br>
</div>
<div>I tried with sigma =1 and epsilon = 0.25 as well for single particle but no success yet. </div>
<div><br>
</div>
<div>Case 1. </div>
<div><br>
</div>
<div><span style="font-size:10pt">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. </span></div>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-size:10pt">The potential energy is 16128 kJ/mol</span></div>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-size:10pt">Case 2.</span></div>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-size:10pt">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 ( </span><span style="font-size:13.3333px">4*epsilon*sigma^6)
values set as 4 .</span></div>
<div><br>
</div>
<div><span style="font-size:13.3333px">The potential energy is 1344 kJ/mol</span></div>
<div><span style="font-size:13.3333px"><br>
</span></div>
<div><span style="font-size:13.3333px">Case 3.</span></div>
<div><span style="font-size:13.3333px"><br>
</span></div>
<div><span style="font-size:10pt">I copied the table 6-12 from the GROMACS top directory as table_A_wall0.xvg and did the same calculation this time with
</span><span style="font-size:13.3333px">wall-type = table option </span><span style="font-size:10pt"> with A (4*epsilon/4*sigma^12) and C ( </span><span style="font-size:13.3333px">4*epsilon/4*sigma^6) values set as 1</span><span style="font-size:13.3333px">.</span></div>
<div><br>
</div>
<div>The potential energy is 336 KJ/mol.</div>
<div><br>
</div>
<div><br>
</div>
<div>In table 6-12 from the GROMACS top directory for r value of 0.5 we have the following values,</div>
<div><br>
</div>
<div>r 1/r 1/r**2 -1/r**6 -6/r**7 1/r**12 12/r**13</div>
<div><br>
</div>
<div>5.0000000000e-01 2.0000000000e+00 4.0000000000e+00 -6.4000000000e+01 -7.6800000000e+02 4.0960000000e+03 9.8304000000e+04</div>
<div><br>
</div>
<div>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.</div>
<div><span style="font-size:10pt"><br>
</span></div>
<div>PS: I also created tables manually and tried both case 2 and 3. The results are same.</div>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-size:10pt">Sorry once again for long email.</span></div>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-size:10pt">Sincerely,</span></div>
<div><span style="font-size:10pt"><br>
</span></div>
<div><span style="font-size:10pt">Sudharsan</span></div>
<div><span style="font-size:10pt"> </span></div>
<div><br>
</div>
<div><br>
</div>
<div><br>
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<div><br>
<div style="font-family:Times New Roman; color:#000000; font-size:16px">
<hr tabindex="-1">
<div id="divRpF836664" style="direction:ltr"><font face="Tahoma" color="#000000" size="2"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">
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" target="_blank">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" target="_blank">hess@kth.se</a>]<br>
<b>Sent:</b> 05 February 2016 16:01<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" 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><br>
</div>
<div>
<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 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" target="_blank">
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" target="_blank"></a><a class="moz-txt-link-abbreviated" 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 class="moz-txt-link-abbreviated" 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 class="moz-txt-link-rfc2396E" href="mailto:sudharsan.pandiyan@chem.kuleuven.be" target="_blank">
</a><a class="moz-txt-link-rfc2396E" 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 class="moz-txt-link-abbreviated" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">
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" target="_blank"></a><a class="moz-txt-link-abbreviated" 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 class="moz-txt-link-abbreviated" href="mailto:sudharsan.pandiyan@chem.kuleuven.be" target="_blank"></a><a class="moz-txt-link-abbreviated" 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 class="moz-txt-link-abbreviated" 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 class="moz-txt-link-abbreviated" href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" target="_blank">
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" target="_blank"></a><a class="moz-txt-link-abbreviated" 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 class="moz-txt-link-abbreviated" href="mailto:hess@kth.se" target="_blank">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" 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>
--<br>
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