Thank you.<br><br>I know general setup to run a simulation, and I'm running one.<br>As you see the title, I have problem with image.<br>I'm getting broken lipid in the trajectory.<br>Would you let me know how to avoid this?
<br>Do I need special setup?<br><br><div class="gmail_quote"><br>On Jan 15, 2008 5:30 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</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;">
<div>Myunggi Yi wrote:<br>> Thank you all of you.<br>><br>> I've got a pre-equilibrated hydrated POPC bilayer from a web-site.<br>> I made a hole, and I placed my protein.<br>> Now, what is the next step?
<br><br></div>If you're asking this, then you'll want to read most of the links from<br>this site <a href="http://wiki.gromacs.org/index.php/Beginners" target="_blank">http://wiki.gromacs.org/index.php/Beginners</a>
, particularly the<br>one listed under "S" :-)<br><br>Note also, that having a "pre-equilibrated" system in a .pdb file is not<br>worth anything much. These don't come with velocities, and so you'd need
<br>to equilibrate them once you generate them. If you changed the box size<br>and added more or less solvent, you'll need to equilibrate that. If<br>you're worried about distorting the system during the equilibration,
<br>that's what position restraints are for. See man pdb2gmx, and chapters 4<br>and 5 of the GROMACS manual.<br><font color="#888888"><br>Mark<br></font><div><div></div><div>_______________________________________________
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</a><br></div></div></blockquote></div><br><br clear="all"><br>-- <br>Best wishes,<br><br>MYUNGGI YI<br>==================================<br>KLB 419<br>Institute of Molecular Biophysics<br>Florida State University<br>Tallahassee, FL 32306
<br><br>Office: (850) 645-1334<br><a href="http://www.scs.fsu.edu/%7Emyunggi" target="_blank">http://www.scs.fsu.edu/~myunggi</a>