normal why i am getting lipid bilayer tail outside and water inside?

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3 months 1 week ago #8187 by sagar
Hello,
I have followed the bilayer-lipidome-tutorial ,but there in lipid bilayer tail part is outside and head part is inside with water.

Same bilayer shown in the link below has formed

www.youtube.com/watch?v=SbWh_XgCHyw

How to solve this problem?

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3 months 1 week ago #8188 by bart
Think about the PBC, shift the box by 1/2 z in your mind and see if you are still surprised by the result.

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3 months 5 days ago #8189 by riccardo
@sagar: note also that the same "issue" was discussed in this other post: cgmartini.nl/index.php/component/kunena/...5677-inverse-bilayer

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3 months 4 days ago #8190 by sagar
But , what command we need to use so it will look proper way?

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3 months 4 days ago #8191 by sagar
Thanks for your quick reply.
Could you please tell me how to shift box by z/2? Or what command we need to use to shift the box by z/2?

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3 months 4 days ago #8192 by riccardo
There are multiple way, e.g., using the Gromacs tool "gmx editconf" (see the "-translate" option).

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3 months 16 hours ago #8198 by sagar
Hello Riccardo,
I tried by using gmx editconf with -translate 7.5 7.5 3.52 but still its not working.

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3 months 16 hours ago #8199 by sagar
I am using VMD for for the visualization. I dont have any idea that How to replicate the box in all directions.
Could you please help in this? I have stuck at this point for long time.

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2 months 3 weeks ago #8201 by riccardo
How to replicate box in VMD: www.researchgate.net/post/VMD_how_to_dis...etitive_periodic_box

Translate coordinates with "gmx_editconf": if you want to translate the bilayer along z (let's say your z is 6 nm) by z/2 (--> 3 nm), this would be the command:

gmx editconf -f bilayer.gro -translate  0  0  3.0  -o translated-bilayer.gro

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2 months 2 weeks ago #8215 by sagar
I tried this one also but still not getting structure shown in the tutorial...still having the same problem. I have followed following commands for dppc bilayer..pls help

$ tar -xzvf bilayer-lipidome-tutorial-GMX5_2017Aug04.tgz

$ cd bilayer-lipidome-tutorial
$ cd spontaneous-assembly/initial_assembly

$ gmx insert-molecules -ci DPPC-em.gro -box 7.5 7.5 7.5 -nmol 128 -radius 0.21 -try 500 -o 128_noW.gro

gmx editconf -f 128_noW.gro -translate 0 0 3.75 -o translated-bilayer.gro

$ [gedit/vi] dppc.top

$ gmx grompp -f minimization.mdp -c 128_noW.gro -p dppc.top -o dppc-min-init.tpr

$ gmx mdrun -deffnm dppc-min-init -v -c 128_minimized.gro

$ gmx solvate -cp 128_minimized.gro -cs water.gro -o waterbox.gro -maxsol 768 -radius 0.21

$ [gedit/vi/other editor] dppc.top

$ gmx grompp -f minimization.mdp -c waterbox.gro -p dppc.top -o dppc-min-solvent.tpr

$ gmx mdrun -deffnm dppc-min-solvent -v -c minimized.gro

$ gmx grompp -f martini_md.mdp -c minimized.gro -p dppc.top -o dppc-md.tpr

$ gmx mdrun -deffnm dppc-md -v

$ gmx view -f dppc-md.xtc -s dppc-md.tpr

$ gmx trjconv -s dppc-md.tpr -f dppc-md.xtc -o dppc-md.pdb -pbc whole -conect

$ pymol dppc-md.pdb

$ chmod +x do_vmd.sh

$ ./do_vmd.sh

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2 months 1 week ago #8218 by xavier
gmx trjconv would be more useful to treat the all trajectory at once and no need to generate new files.

try to translate the trajectory on the z direction by half the size of the z dimension (X in nm) and put the molecules back into the box:

gmx trjconv -f traj.xtc -trans 0 0 X -pbc mol -s traj.tpr -o traj_centered.xtc

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2 months 1 week ago #8222 by sagar
I tried this i have changes my command of trjconv but still not getting ...
I have followed following commands

$ tar -xzvf bilayer-lipidome-tutorial-GMX5_2017Aug04.tgz

$ cd bilayer-lipidome-tutorial
$ cd spontaneous-assembly/initial_assembly

$ gmx insert-molecules -ci DPPC-em.gro -box 7.5 7.5 7.5 -nmol 128 -radius 0.21 -try 500 -o 128_noW.gro

gmx editconf -f 128_noW.gro -translate 0 0 3.75 -o translated-bilayer.gro

$ [gedit/vi] dppc.top

$ gmx grompp -f minimization.mdp -c 128_noW.gro -p dppc.top -o dppc-min-init.tpr

$ gmx mdrun -deffnm dppc-min-init -v -c 128_minimized.gro

$ gmx solvate -cp 128_minimized.gro -cs water.gro -o waterbox.gro -maxsol 768 -radius 0.21

$ [gedit/vi/other editor] dppc.top

$ gmx grompp -f minimization.mdp -c waterbox.gro -p dppc.top -o dppc-min-solvent.tpr

$ gmx mdrun -deffnm dppc-min-solvent -v -c minimized.gro

$ gmx grompp -f martini_md.mdp -c minimized.gro -p dppc.top -o dppc-md.tpr

$ gmx mdrun -deffnm dppc-md -v

$ gmx view -f dppc-md.xtc -s dppc-md.tpr

$ gmx trjconv -f dppc-md.xtc -trans 0 0 3.75 -pbc mol -s dppc-md.tpr -o traj_centered.xtc

gmx trjconv -s dppc-md.tpr -f traj_centered.xtc -o dppc-md.pdb

$ pymol dppc-md.pdb

$ chmod +x do_vmd.sh

$ ./do_vmd.sh

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2 months 1 week ago #8224 by xavier
Well ... your list of commands is a little confusing to be honest.

My impression is that the trjconv command I suggest should work. Not sure what is happening.

may be you should replace "-pbc mol" by "-pbc inbox". That should put the atoms in the box after translating them. Then run the "-pbc mol" on the new trajectory without translating again :)).

It could also be that running the modifications one by one could help. That is:
- first translate
- then run the pbc option, trying the mol and inbox options.

One of those combination should work.

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