[gmx-users] How to generate a new xtc file with a membrane protein complex properly oriented along a given axis?

ABEL Stephane Stephane.ABEL at cea.fr
Wed Oct 24 11:38:34 CEST 2018

Hello All, 

I have  basic questions regarding the procedure to generate an new xtc where a membrane protein inserted a detergent micelle is properly oriented for the computation of 2D density Map. Indeed for this calculation I need to have the protein-surfactant complex properly oriented along a given axis (say Z). For this I chose two atoms and define a vector in my protein and I would like that this vector // to z axis. How to this in GROMACS? I think that editconf can do the trick, however I notice that this tool cannot use and output an xtc file. So is there an alternative approach ? If yes how (an example of command line will be very useful) 

Thanks in advance


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