[gmx-users] Multiple position restraints on the same system
NG HUI WEN
HuiWen.Ng at nottingham.edu.my
Wed Oct 27 04:17:29 CEST 2010
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
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
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