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why i am getting lipid bilayer tail outside and water inside?
- sagar
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4 years 9 months ago #8187
by sagar
why i am getting lipid bilayer tail outside and water inside? was created 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?
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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- bart
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4 years 9 months ago #8188
by bart
Replied by bart on topic why i am getting lipid bilayer tail outside and water inside?
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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- riccardo
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4 years 9 months ago #8189
by riccardo
Replied by riccardo on topic why i am getting lipid bilayer tail outside and water inside?
@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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- sagar
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4 years 9 months ago #8190
by sagar
Replied by sagar on topic why i am getting lipid bilayer tail outside and water inside?
But , what command we need to use so it will look proper way?
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4 years 9 months ago #8191
by sagar
Replied by sagar on topic why i am getting lipid bilayer tail outside and water inside?
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?
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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- riccardo
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4 years 9 months ago #8192
by riccardo
Replied by riccardo on topic why i am getting lipid bilayer tail outside and water inside?
There are multiple way, e.g., using the Gromacs tool "gmx editconf" (see the "-translate" option).
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4 years 9 months ago #8198
by sagar
Replied by sagar on topic why i am getting lipid bilayer tail outside and water inside?
Hello Riccardo,
I tried by using gmx editconf with -translate 7.5 7.5 3.52 but still its not working.
I tried by using gmx editconf with -translate 7.5 7.5 3.52 but still its not working.
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4 years 9 months ago #8199
by sagar
Replied by sagar on topic why i am getting lipid bilayer tail outside and water inside?
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.
Could you please help in this? I have stuck at this point for long time.
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4 years 8 months ago #8201
by riccardo
Replied by riccardo on topic why i am getting lipid bilayer tail outside and water inside?
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:
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.groPlease Log in or Create an account to join the conversation.
- sagar
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4 years 8 months ago #8215
by sagar
Replied by sagar on topic why i am getting lipid bilayer tail outside and water inside?
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
$ 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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4 years 8 months ago #8218
by xavier
Replied by xavier on topic why i am getting lipid bilayer tail outside and water inside?
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
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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4 years 8 months ago #8222
by sagar
Replied by sagar on topic why i am getting lipid bilayer tail outside and water inside?
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
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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- xavier
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4 years 8 months ago #8224
by xavier
Replied by xavier on topic why i am getting lipid bilayer tail outside and water inside?
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.
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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