<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div><span class="Apple-style-span" style="font-family: times, serif; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> I am using MARTINI coarse-grained force-field to study interaction of a transmembrane peptide WALP or KALP in a lipid-bilayer. So,I was planning to insert a martini KALP or WALP peptide inside a martini DPPC bilayer in a transmembrane manner. For that purpose, I was going through the <span class="yshortcuts" id="lw_1286913212_0" style="color: rgb(54, 99, 136); ">MARTINI</span> JCTC paper( vol.4 , page-819 ) introducing the protein force-field where a simulation study of KALP peptide in a bilayer has
been discussed ( in page 828 of that paper) . But, I did not get any details how the KALP or WALP peptide are inserted in a bilayer as initial configuration.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">So, I was wondering if I can get some help on how to insert this WALP peptide in to Martini DPPC bilayer . I guess, there may be some way of pulling , that may do the trick, but I am not sure how to keep it trans-membrane as well during pulling . So, Any suggestions will be helpful. </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sanku</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div
style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">P.S:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I tried MARTINI coarse-grained simulation if the WALP peptide can get spontaneously inserted in a 128-lipid DPPC bilayer( after starting from a bulk water phase) in a transmembrane manner . But, looks like it does not get inserted in bilayer in a transmembrane manner, after 500 ns simualtion. At the most, they remain in the interface of water and <span class="yshortcuts" id="lw_1286913212_1" style="color: rgb(54, 99, 136); border-bottom-style: dotted; border-bottom-width: 2px; border-bottom-color: rgb(54, 99, 136); cursor: pointer; ">lipids</span>. I ran multiple configurations but in some cases it goes other side of membrane. in some cases, it remained parallel in
interface.but never got inserted in a trans-membrane manner.</div><div><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "></div></span></div><div style="position:fixed"></div>
</div><br>
</body></html>