[gmx-users] Convert-tpr pbc problem for membrane protein

[wh]

Dear Gromacs users,

 

I recently used Charmm-gui Gromacs input generator to build some input files
for a membrane protein system and ran several simulation with them.
Recommended by charmm-gui README file I used convert-tpr to perform
continuous simulation. Thus the trajectory itself will have some crazy
behavior, with protein in parts and lipid deformed. I managed to restore the
protein and generate a trajectory with just protein. However, now I have a
problem to  transform the whole system including lipid and water, ions. No
matter what I tried the lipid will still have a bizarre shape. Does anyone
have experience with this issue? Any suggestion will be greatly appreciated.
Thanks!

 

Han