Hi Fernando,<br>
<br>
Have a look at the two parameter files and see in which regard they are
different, for indeed they are. Energy minimization is a distinct
process, for which you need specific settings in the .mdp file and also
have other control parameters. One of the most important settings
concerns the integrator, for which you can choose several integrators
for energy minimization (e.g. steep, l-bfgs), molecular dynamics (md)
and others (check the manual). <br><br>
Cheers,<br>
<br>
Tsjerk<br>
<br><div><span class="gmail_quote">On 10/4/05, <b class="gmail_sendername">MGiò</b> <<a href="mailto:magiofer@gmail.com">magiofer@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;">
HI!<br>
<br><div><span class="q"><span class="gmail_quote">On 10/4/05, <b class="gmail_sendername">Fernando Mattio</b> <<a href="mailto:mattiofer@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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></span><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><span class="q"><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></span><div><br>
usually I set different energy groups in presence of the solvent (Protein and SOL)<br>
</div><span class="q"><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... That´s why I am asking
these things.</blockquote></span><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;"><span class="q">
Thank you very much in advance!<br><span>
Fernando Mattio<br>
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<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>