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normal 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.

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Does anybody have any idea how to solve this problem?

Thank you very much.

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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).

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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.

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