<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 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">å Exp[-2A(r-r*)] -2 </span><span style="background-color:rgb(249,249,249);font-family:sans-serif;line-height:19px">å
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">å
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">å
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 href="http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials#Constructing_the_Table(s)" 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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