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cant add enough water to dppc vesicle box
- msaeedi
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10 years 9 months ago #1778
by msaeedi
cant add enough water to dppc vesicle box was created by msaeedi
I do the simulation as RAMDOM-I in the thesis "Molecular Dynamics Simulation of
the Formation, Structure, and Dynamics of Small Phospholipid Vesicles"
using martini_v2.1.itp force field. I must insert 1500 dppc lipid and 400000 cg water in cubic box of 25 nm but there are about 150000 cg water in .gro file and I can't add more water in the box?
Can you help me to add exact 400000 in the box?
the Formation, Structure, and Dynamics of Small Phospholipid Vesicles"
using martini_v2.1.itp force field. I must insert 1500 dppc lipid and 400000 cg water in cubic box of 25 nm but there are about 150000 cg water in .gro file and I can't add more water in the box?
Can you help me to add exact 400000 in the box?
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- msaeedi
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10 years 9 months ago #1783
by msaeedi
Replied by msaeedi on topic cant add enough water to dppc vesicle box
I do the simulation as RAMDOM-I in the thesis "Molecular Dynamics Simulation of
the Formation, Structure, and Dynamics of Small Phospholipid Vesicles"
using martini_v2.1.itp force field. I must insert 1500 dppc lipid and 400000 cg water in cubic box of 25 nm but there are about 150000 cg water in .gro file and I can't add more water in the box?
Can you help me to add exact 400000 in the box?
the Formation, Structure, and Dynamics of Small Phospholipid Vesicles"
using martini_v2.1.itp force field. I must insert 1500 dppc lipid and 400000 cg water in cubic box of 25 nm but there are about 150000 cg water in .gro file and I can't add more water in the box?
Can you help me to add exact 400000 in the box?
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- djurre
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10 years 9 months ago #1784
by djurre
Replied by djurre on topic cant add enough water to dppc vesicle box
I'm not familiar with the particular simulation you mention, but I assume you use genbox to add water to the system. A few things you can try:
-Make the starting box bigger.
-Use a smaller -vdwd for genbox.
-Make the starting box bigger.
-Use a smaller -vdwd for genbox.
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- xavier
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10 years 9 months ago #1785
by xavier
Replied by xavier on topic cant add enough water to dppc vesicle box
You could alternatively copy the original water box on two directions to get 4*150000 molecules. This is possible with genconf, which is part of gromacs.
djurre wrote: I'm not familiar with the particular simulation you mention, but I assume you use genbox to add water to the system. A few things you can try:
-Make the starting box bigger.
-Use a smaller -vdwd for genbox.
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