Hi Peggy,<br><br>To understand the differencxes between the runs, you'll have to read and compare the .mdp files well. I'd suggest to start with the Gromacs manual, chapter 7. For one, position restraint MD depends on the presence of [ position_restraints ] in the topology and has nothing to do with the length of the run. Please do some more background reading on MD. Often, inclusion of the [ position_restraints ] is controlled in the .mdp file by adding a define statement (-DPOSRES).
<br><br>Why Bonvin uses so many steps of energy minimization and position restraint MD is unclear to me. For a normal MD simulation it's not necessary. A fairly common scheme used is:<br><br>1. EM in vacuum<br>2. EM in solvent
<br>3. PR MD<br>4. NVT MD equilibration<br>5. NPT MD equilibration<br>6. Production run<br><br>You could have a look at the following tutorial rather than Bonvins: <a href="http://www.nmr.chem.uu.nl/~tsjerk/MDCourse/">http://www.nmr.chem.uu.nl/~tsjerk/MDCourse/
</a><br><br>Hope it helps,<br><br>Tsjerk<br><br><br><div class="gmail_quote">On Nov 20, 2007 6:29 AM, Peggy Yao <<a href="mailto:peggy.yao@gmail.com">peggy.yao@gmail.com</a>> 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 am new to Gromacs. I am following this tutorial:<br><a href="http://www.nmr.chem.uu.nl/%7Eabonvin/tutorials/MD-Data/index.html" target="_blank">http://www.nmr.chem.uu.nl/~abonvin/tutorials/MD-Data/index.html</a>
. My<br>question is: why it has multiple steps of energy minimization and<br>position restrained simulation? Is that a common practice? What's the<br>key difference among these steps?<br><br>Thanks!<br><br>Peggy<br>_______________________________________________
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>
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