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<div class="moz-cite-prefix">Hi,<br>
<br>
I would suggest to use the Buckingham functionalilty, set C6 to
zero and modify lines 957-959 of src/mdlib/tables.c to fill the
table with your potential instead of exp(-a*r).<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 10/17/2013 01:30 PM, Mark Abraham wrote:<br>
</div>
<blockquote
cite="mid:CAMNuMAS0DBWEAzLUUEuto+UiO=+UWc3syquS-iO1iTfuV3-ncg@mail.gmail.com"
type="cite">
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<div dir="ltr">Hi,
<div><br>
</div>
<div>It's hard to make any sense of the formatting of your
equations, and you haven't said what over what quantity your A
varies or what r and r* are... Do check out manual sections
4.2.13 and 6.9.</div>
<div><br>
</div>
<div>Mark</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, Oct 15, 2013 at 10:02 PM, Reza
Ghafarian Shirazi <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:rezagh@student.uef.fi"
target="_blank">rezagh@student.uef.fi</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Dear all,
<div><br>
</div>
<div>I'm trying to define modified morse potential in
Gromacs to be used as a forcefield using tabulated
potentials.</div>
<div><br>
</div>
<div>My potential's functional form is as: <span
style="background-color:rgb(249,249,249);font-family:sans-serif;line-height:19px">ε
Exp[-2A(r-r*)] -2 </span><span
style="background-color:rgb(249,249,249);font-family:sans-serif;line-height:19px">ε
Exp[-A(r-r*)]</span></div>
<div><span
style="background-color:rgb(249,249,249);font-family:sans-serif;line-height:19px"><br>
</span></div>
<div><span style="background-color:rgb(249,249,249)"><font
face="sans-serif"><span style="line-height:19px">So
I have to define g® = </span></font></span><span
style="background-color:rgb(249,249,249);font-family:sans-serif;line-height:19px">ε
Exp[</span><span
style="background-color:rgb(249,249,249)"><font
face="sans-serif"><span style="line-height:19px">-2A(r-r*)]
and h®=</span></font></span><span
style="background-color:rgb(249,249,249);font-family:sans-serif;line-height:19px">-2 </span><span
style="background-color:rgb(249,249,249)"><font
face="sans-serif"><span style="line-height:19px">ε
Exp[-A(r-r*)]. They have to be defined as
values in a xvg table where the table is filled
with values of r, f®, f'®, g®,….</span></font></span></div>
<div><font face="sans-serif"><span
style="line-height:19px">My question is how can I
make vales of these functions, while there's a
variable in the exponential term. </span></font></div>
<div><font face="sans-serif"><span
style="line-height:19px">I saw in the manual on the </span></font><a
moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials#Constructing_the_Table%28s%29"
target="_blank">website</a><font face="sans-serif"><span
style="line-height:19px"> noting that h® for
buckingham is expressed as h®=AExp[-Br] so I was
wondering how they make the table of h® values while
B is a variable.</span></font></div>
<div><font face="sans-serif"><span
style="line-height:19px"><br>
</span></font></div>
<div><font face="sans-serif"><span
style="line-height:19px">Solutions which cam ego my
mind were:</span></font></div>
<div><font face="sans-serif"><span
style="line-height:19px">Should we use some </span></font><span
style="font-family:sans-serif;line-height:19px">mathematical
approximations like Exp[-u]=1-u.</span></div>
<div><font face="sans-serif"><span
style="line-height:19px">or simply tabulated
potentials does not support potentials more complex
than lennard jones, and Buckingham is an integrated
feature which doesn't need the xvv table.</span></font></div>
<div><font face="sans-serif"><span
style="line-height:19px">Any suggestions will be
appreciated</span></font></div>
<div><font face="sans-serif"><span
style="line-height:19px"><br>
</span></font></div>
<div><font face="sans-serif"><span
style="line-height:19px">regards</span></font></div>
<span class="HOEnZb"><font color="#888888">
<div><font face="sans-serif"><span
style="line-height:19px">Reza </span></font></div>
</font></span></div>
<br>
--<br>
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