HI!<br>
<br><div><span class="gmail_quote">On 10/4/05, <b class="gmail_sendername">Fernando Mattio</b> <<a href="mailto:mattiofer@gmail.com">mattiofer@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear gromacs users,<br>
<br>
I have doubts about parameter file: Should I use the same parameter
file before and after the energy minimization or do I have to change
it? </blockquote><div><br>
do you mean the same parameters fo mechanics and dynamics? you have to
change your .mdp, of course. you have to use md as the integrator
and set temperature and temperature coupling method, at least, if you
want to run NVT MD.<br>
</div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">And if I create a solvent box do I have to change anything in my
parameter file? </blockquote><div><br>
usually I set different energy groups in presence of the solvent (Protein and SOL)<br>
</div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">I am following the Introduction to Molecular Dynamics
course on <a href="http://md.chem.rug.nl/education/mdcourse2004" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://md.chem.rug.nl/education/mdcourse2004</a> and in this
course they used 2 different parameter files... Thatīs why I am asking
these things.</blockquote><div><br>
anyway the fullmd_sol.mdp that you find in the course you're following is clear and complete.<br>
</div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Thank you very much in advance!<br><span class="sg">
Fernando Mattio<br>
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