[gmx-users] How to incorporate WALP and KALP peptide in a Martini bilayer

Sanku M msanku65 at yahoo.com
Tue Oct 12 21:58:31 CEST 2010

  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 MARTINI 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.
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. 



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 lipids. 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 

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