I ask you for help. I hope you will help me.
I created my DOPC membrane
I have a question. I try to center my membrane after production (md_0_1.gro). I try to use
gmx trjconv -s md_0_1.tpr -f md_0_1.trr -o md_0_1_noPBC.gro -pbc mol -center
And I choose 2 DOPC and next 0 System and still have the same picture, when I show .gro file in vmd. (picture title: “after trjconv”)
gmx editconf -f md_0_1.gro -o md_0_1_translate.gro -translate 0 0 4
(picture title: “after translate”)
And still I have the same view in vmd and I don’t know why.
I also try this, but still I have the same view in my vmd program
gmx editconf -f md_0_1.gro -o md_0_1_new.gro -center 0 0 0
Read 34242 atoms
Volume: 424.127 nm^3, corresponds to roughly 190800 electrons
Velocities found
system size : 8.892 9.466 8.843 (nm)
center : 3.346 3.249 4.282 (nm)
box vectors : 6.516 6.515 9.991 (nm)
box angles : 90.00 90.00 90.00 (degrees)
box volume : 424.13 (nm^3)
shift : 1.654 1.751 2.718 (nm)
new center : 5.000 5.000 7.000 (nm)
And still I have the same view in vmd and I don’t know why.
Why water always go to the center of the box?
I want my membrane molecules in the center, not water.
Well, hopefully, this was equilibrated thoroughly, because your structure before minimization has large and problematic gaps.
That aside, to answer your actual question, I'd create an index group for your lipid atoms in an index.ndx file through the following command:
gmx make_ndx -f md_0_1.gro -o index.ndx
In the interactive part, I'd say, "r DOPC" to signify that I want to select all the DOPC atoms. Then I'd type "q" and hit enter to save the index.ndx file.
Then, I'd center the file based on that DOPC index group using gmx editconf and the -c flag (for center) with a command like below.
gmx editconf -f md_0_1.gro -n index.ndx -o md_bilayer_centered.gro -pbc -c
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