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Protein coming out from box in a lipid-protein system
- ROY
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2 years 4 months ago #9239
by ROY
Protein coming out from box in a lipid-protein system was created by ROY
Dear All,
I have started getting insight in membrane-protein system/ simulation. The system has DOPC lipid membrane (x*y=100*100 nm) and thee units of protein dimer. Initially, the protein molecules are placed ~5 nm away from the membrane edge; proteins are also far apart.
At the end of 500 ns simulation, I found one of the protein molecule coming out from the box while other two are in close proximity of membrane. The following command used for PBC correction:
gmx trjconv -s sys.tpr -f sys.xtc -pbc cluster -center -o sys_PBC.xtc
where, clustering and centering is done by considering protein and membrane respectively.
Is there anything wrong in my simulation or PBC correction which I overlooked ? However, my water box is quite large (10 nm from membrane edge along the membrane normal).
Look forward to your comment/ suggestion. Your help will be highly appreciated.
Thank you.
Regards,
Priti
I have started getting insight in membrane-protein system/ simulation. The system has DOPC lipid membrane (x*y=100*100 nm) and thee units of protein dimer. Initially, the protein molecules are placed ~5 nm away from the membrane edge; proteins are also far apart.
At the end of 500 ns simulation, I found one of the protein molecule coming out from the box while other two are in close proximity of membrane. The following command used for PBC correction:
gmx trjconv -s sys.tpr -f sys.xtc -pbc cluster -center -o sys_PBC.xtc
where, clustering and centering is done by considering protein and membrane respectively.
Is there anything wrong in my simulation or PBC correction which I overlooked ? However, my water box is quite large (10 nm from membrane edge along the membrane normal).
Look forward to your comment/ suggestion. Your help will be highly appreciated.
Thank you.
Regards,
Priti
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