[gmx-users] lipid membrane study and the increase in z dimension on dppc128.gro

rama david ramadavidgroup at gmail.com
Fri Oct 10 08:02:33 CEST 2014

Dear Friends,
      I want to do the simulation of lipid membrane with peptides. Peptide
concist  8 amino acid.I want to keep the two or four peptide just away from
membrane and
want to see how they interact with membrane.
          I choose the DPPC membrane for the work ( from D.Peter Tieleman ).
 I am following the Justin tutorials for the work flow.

 Problems are  as per follow :

         The size of dppc128.gro is very small on z-axis to put my two or
four peptide
( peptide is made of 8 amino acid). So I want to increase the size of
dppc128.gro on z axis. so I can put two or four peptide peptide.
       Please tell me how to do it ??

 In my biological and other study I seen that  peptide forms the beta sheet
structure and react with plasma membrane. Is it possible to show this
effect with the DPPC lipid membrane or should I change in protocol and

I will be thankful for your suggestion.
I am eagerly waiting for your reply

With best regards,
Prashant Kurkute.

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