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

[Dallas Warren]

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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