Dear GMXusers,

 

I am trying to perform NVT on my solvated protein-lipid system. After
inserting the protein into the lipid using inflategro and a round of
energy minimization, I performed a 100ps NVT with position restraint
only on the protein molecule using (posre.itp).

 

After 100ps of NVT, the bilayer separated. As a result, I am now trying
to redo the NVT step, this time probably with position restraints on the
protein AND the P8 atom of my POPC (lipid_posre.itp). 

 

I have in my .top file

;Protein

#include "protein.itp"

#ifdef POSRES

#include "posre.itp"

#endif

 

;Lipid

#include"popc.itp"

#ifdef POSRES_LIPID

#include "lipid_posre.itp"

#endif

 

When it comes to the .mdp file, I wonder how do I include both 

define = -DPOSRES and define = -DPOSRES_LIPID ? 

 

Another quick question, is it advisable to do "trjconv -pbc mol" on my
system after every energy minimization/ MD to get an unbroken structure
before I carry on further?

 

Thanks a lot

 

HW

 

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