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pbc problem
- albumns
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6 years 11 months ago #7241
by albumns
pbc problem was created by albumns
Hello,
I try to visualize a .gro file from Martini simulation. However, I noticed that the lipids always above the water molecule and my protein split into two. Even after I run the following command:
gmx trjconv -s dppc-md.tpr -f dppc-md.gro -pbc whole -dump 0 -o dppc-md-pbc.gro
The issue is still there.
Here is a snapshot for my problem:
This image is hidden for guests.
Does anybody have any idea how to solve this problem?
Thank you very much.
I try to visualize a .gro file from Martini simulation. However, I noticed that the lipids always above the water molecule and my protein split into two. Even after I run the following command:
gmx trjconv -s dppc-md.tpr -f dppc-md.gro -pbc whole -dump 0 -o dppc-md-pbc.gro
The issue is still there.
Here is a snapshot for my problem:
This image is hidden for guests.
Please log in or register to see it.
Does anybody have any idea how to solve this problem?
Thank you very much.
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- Pim
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6 years 11 months ago #7246
by Pim
Replied by Pim on topic pbc problem
I'd say -pbc mol should work better than -pbc whole
If you want everything in the middle of your box, you could also use trjconv -fit trans to fit e.g. the BB beads of a protein on your starting structure (assuming it starts in the middle).
If you want everything in the middle of your box, you could also use trjconv -fit trans to fit e.g. the BB beads of a protein on your starting structure (assuming it starts in the middle).
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- albumns
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6 years 11 months ago #7247
by albumns
Replied by albumns on topic pbc problem
problem solved after I used both -translate and -center option.
Many thanks for advices.
Many thanks for advices.
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