- Posts: 13
Why I got water in the centre with DPPC on the two sides?
- lanselibai
- Topic Author
- Offline
- Fresh Boarder
Less
More
5 years 3 months ago #7984
by lanselibai
Why I got water in the centre with DPPC on the two sides? was created by lanselibai
I am following the exactly same as "Bilayer self-assembly" in the
cgmartini.nl/index.php/tutorials-general...n-gmx5/bilayers-gmx5
However, after the 30 ns, I got water molecules in the centre with DPPC on the two ends.
Is this normal?
Here is my graph
github.com/lanselibai/martini/blob/master/1.png
However, after the 30 ns, I got water molecules in the centre with DPPC on the two ends.
Is this normal?
Here is my graph
github.com/lanselibai/martini/blob/master/1.png
Please Log in or Create an account to join the conversation.
- bart
- Offline
- Admin
Less
More
- Posts: 98
5 years 3 months ago #7990
by bart
Replied by bart on topic Why I got water in the centre with DPPC on the two sides?
You didn't take the PBC into account. All is fine if you shift the box with half z.
Please Log in or Create an account to join the conversation.
- riccardo
- Offline
- Platinum Boarder
5 years 3 months ago #7991
by riccardo
Replied by riccardo on topic Why I got water in the centre with DPPC on the two sides?
Indeed.
@lanselibai : see also this thread:
cgmartini.nl/index.php/component/kunena/...5677-inverse-bilayer
@lanselibai : see also this thread:
cgmartini.nl/index.php/component/kunena/...5677-inverse-bilayer
Please Log in or Create an account to join the conversation.
- lanselibai
- Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 13
5 years 3 months ago #7992
by lanselibai
Replied by lanselibai on topic Why I got water in the centre with DPPC on the two sides?
Thank you very much! I got that!
Please Log in or Create an account to join the conversation.
- TravisM
- Offline
- Fresh Boarder
Less
More
- Posts: 6
4 years 4 months ago #8388
by TravisM
Replied by TravisM on topic Why I got water in the centre with DPPC on the two sides?
Hi all,
I apologize for ressurecting an old thread, but I figured it was better than creating a new thread for the exact same topic.
My simulation resulted in the same situation (lipid-lipid interaction spans pbc) - however, I cannot for the life of me figure out how to adjust the trajectories to center everything. I have tried many combinations of
gmx trjconv -f .xtc -s .tpr -o .gro -trans 3.75 0 0
OR
gmx trjconv -f .xtc -s .tpr -o .gro -shift 3.75 0 0
With different x values for the shift/translate vector without observing any changes when visualizing the system in VMD. I was able to get a visualization of the bilayer using -pbc res as an option to trjconv. However, this placed a series of headgroups along the boundary and all of the water molecules on a single side. For aesthetic purposes I would love to get a trajectory where the water beads are located at the edges of the simulation box with the lipids in the center.
I am brand new to Linux/GROMACS/MARTINI so if nothing else I figured this is good experience learning to manipulate pbcs.
Thanks!
Travis
I apologize for ressurecting an old thread, but I figured it was better than creating a new thread for the exact same topic.
My simulation resulted in the same situation (lipid-lipid interaction spans pbc) - however, I cannot for the life of me figure out how to adjust the trajectories to center everything. I have tried many combinations of
gmx trjconv -f .xtc -s .tpr -o .gro -trans 3.75 0 0
OR
gmx trjconv -f .xtc -s .tpr -o .gro -shift 3.75 0 0
With different x values for the shift/translate vector without observing any changes when visualizing the system in VMD. I was able to get a visualization of the bilayer using -pbc res as an option to trjconv. However, this placed a series of headgroups along the boundary and all of the water molecules on a single side. For aesthetic purposes I would love to get a trajectory where the water beads are located at the edges of the simulation box with the lipids in the center.
I am brand new to Linux/GROMACS/MARTINI so if nothing else I figured this is good experience learning to manipulate pbcs.
Thanks!
Travis
Please Log in or Create an account to join the conversation.
- riccardo
- Offline
- Platinum Boarder
4 years 3 months ago #8394
by riccardo
Replied by riccardo on topic Why I got water in the centre with DPPC on the two sides?
Hi, please have a look at this thread about the same issue
www.cgmartini.nl/index.php/component/kun...ide-and-water-inside
Please Log in or Create an account to join the conversation.
Time to create page: 0.101 seconds