[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
Thu Oct 25 17:38:01 CEST 2018

Thank you very much Dallas, it worked. 



Haven't tried it, but seems to me you generate a .tpr file with the
protein orientated correctly within the box, then use trjconv -fit

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Wed, 24 Oct 2018 at 20:38, ABEL Stephane <Stephane.ABEL at cea.fr> wrote:
> 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
> Stephane
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