Dear all,<br><br>Have anyone tried using CHARMM36 equilibrated POPE bilayer by Dr.Klauda <a href="http://terpconnect.umd.edu/~jbklauda/research/download.html">http://terpconnect.umd.edu/~jbklauda/research/download.html</a>?<br>
<br>I am planning to use the membrane patch for a transmembrane protein simulation. At first visualization, the membrane patch consists of a bilayer with a single layer of water and then several lipids sticking out from the opposite side of the water. So I presumed that to be an effect of PBC.<br>
<br>How can I correct this in Gromacs?<br><br>I've generated a .tpr for the system to use trjconv to manipulate the PBC box.<br clear="all"><br>Out of all the combinations of pbc treatments, this one works:<br><br>trjconv -f pope80-c36box.gro -o pope80_pbc10.gro -s pope80.tpr -pbc mol<br>
<br>This puts the center of mass of the molecules in the box so I got a lipid bilayer with a single, thick layer of water. <br>then followed by <br><br>trjconv -f pope80_pbc10.gro -o pope80_pbc11.gro -s pope80.tpr -pbc mol -center<br>
<br>to center the membrane on POPE.<br><br>The result looks fine (a hydrated bilayer) but I'm a new user to Gromacs so I just wanted to ask if the workflow is reasonable.<br><br>-- <br>Regards,<br>Ariel.<br><br>