<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<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
cite="mid:4A1AE85DA03CB144A9DE9FCDD245E17D2190BE9C@ICTS-S-MBX7.luna.kuleuven.be"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<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>
</div>
<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">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>
<b>Sent:</b> 05 February 2016 16:01<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:gmx-developers@gromacs.org">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>
</div>
<blockquote type="cite">
<style type="text/css" id="owaParaStyle"></style>
<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 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 moz-do-not-send="true"
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
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"
target="_blank"><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>]
on behalf of Berk Hess [<a moz-do-not-send="true"
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
moz-do-not-send="true"
class="moz-txt-link-rfc2396E"
href="mailto:sudharsan.pandiyan@chem.kuleuven.be"
target="_blank">
<a class="moz-txt-link-rfc2396E" href="mailto:sudharsan.pandiyan@chem.kuleuven.be"><sudharsan.pandiyan@chem.kuleuven.be></a></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 moz-do-not-send="true"
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
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"
target="_blank"><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>]
on behalf of Sudharsan Pandiyan [<a
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:sudharsan.pandiyan@chem.kuleuven.be"
target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:sudharsan.pandiyan@chem.kuleuven.be">sudharsan.pandiyan@chem.kuleuven.be</a></a>]<br>
> Sent: 05 February 2016 11:08<br>
> To: <a moz-do-not-send="true"
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 moz-do-not-send="true"
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
moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se"
target="_blank"><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>]
on behalf of Berk Hess [<a moz-do-not-send="true"
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 moz-do-not-send="true"
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>
Gromacs Developers mailing list<br>
<br>
* Please search the archive at <a
moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List"
target="_blank">
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a></a>
before posting!<br>
<br>
* Can't post? Read <a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">
http://www.gromacs.org/Support/Mailing_Lists</a><br>
<br>
* For (un)subscribe requests visit<br>
<a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers"
target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a>
or send a mail to
<a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:gmx-developers-request@gromacs.org"
target="_blank">
gmx-developers-request@gromacs.org</a>.<br>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader" target="_blank"></fieldset>
<br>
</blockquote>
<br>
</div>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>