Re: [gmx-users] trjconv center on protein

Dear Tsjerk, I was afraid that it works like this... It is possible to "center" the system in a different way? without this additional component to the water displacement? What I want is to have protein always in the center of my view But not by some artificial "centering" inside the box nor chang

Re: [gmx-users] trjconv center on protein

Hey :) Option -center shifts the system, which will show up as a component in the displacement. Cheers, Tsjerk On May 6, 2011 5:39 PM, "Justin A. Lemkul" wrote: Tomek Wlodarski wrote: > > Dear Justin, > > Thanks, sure I will give more details. > > This comman... Are all the measurements being

Re: [gmx-users] trjconv center on protein

Tomek Wlodarski wrote: Dear Justin, Thanks, sure I will give more details. This command I've used for trajectory conversion: trjconv -pbc mol -center -s protein.tpr -f old.trr -o new.trr Then I was analysing a new and old trajectory in VMD with my own script. I have noticed that in old traj

Re: [gmx-users] trjconv center on protein

Dear Justin, Thanks, sure I will give more details. This command I've used for trajectory conversion: trjconv -pbc mol -center -s protein.tpr -f old.trr -o new.trr Then I was analysing a new and old trajectory in VMD with my own script. I have noticed that in old trajectory water234 between fra

Re: [gmx-users] trjconv center on protein

Tomek Wlodarski wrote: Hi all! I have a trajectory of simulation (protein in box of water) and I would like to have all the time protein in the center of the water box, becasue protein is drifting to the edge during simulation and I am calculating some properties of water arround the protein.

[gmx-users] trjconv center on protein

Hi all! I have a trajectory of simulation (protein in box of water) and I would like to have all the time protein in the center of the water box, becasue protein is drifting to the edge during simulation and I am calculating some properties of water arround the protein. I was playing with trjconv