well if I need to add it by myself, I am not very sure in what variable to add it to. Like I said, I know to add the force on the atom i do f[indxofatom][XX]= forcevalue, where to potential value due to this force?<br><br>
thanks<br>sikandar<br><br><div class="gmail_quote">On Wed, Mar 24, 2010 at 10:52 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5">On 25/03/2010 2:42 PM, Sikandar Mashayak wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi<br>
<br>
I want to do Coarse-Grained simulation in Gromacs. I have one CG force<br>
formula, which I plan to implement by adding a short code in do_force()<br>
routine in Gromacs 4.0.7 source code.<br>
<br>
After browsing through the do_force() code, I am now familiar with data<br>
structure relevant to add the new force. I mean, I can specify new force<br>
by adding to f[indx][XX] and so on.<br>
<br>
But I am not very sure about potential, whether do I have to explicitly<br>
specify the potential on atoms due to this force or gromacs<br>
automatically takes care of it by knowing the forces on each atoms?<br>
</blockquote>
<br></div></div>
You will need to add that yourself if you want the reported potential to be accurate. GROMACS uses the given parameters in its inner loops to calculate energies and forces. The former are not reverse-engineered from the latter. If the potential is never used, however, then you can forget about it...<br>
<br>
Mark<br><font color="#888888">
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