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Defining box location in INSANE
- peter
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2 years 6 months ago #9169
by peter
Defining box location in INSANE was created by peter
Hello everyone,
Is it possible to define the box locations in INSANE while adding solvent and ions?
I had to add ligands to the system after embedding the protein into the membrane. However, as I add the solvent after this, the molecules get added to only one side of the membrane, whereas the other side remains vacant.
Is there any way to remediate this? If not, can someone please suggest an alternative tool for the same?
Thanks!
Is it possible to define the box locations in INSANE while adding solvent and ions?
I had to add ligands to the system after embedding the protein into the membrane. However, as I add the solvent after this, the molecules get added to only one side of the membrane, whereas the other side remains vacant.
Is there any way to remediate this? If not, can someone please suggest an alternative tool for the same?
Thanks!
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- tsjerk
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2 years 6 months ago #9170
by tsjerk
Replied by tsjerk on topic Defining box location in INSANE
Hi Peter,
Boxes have no location. The system is periodic, infinite and translation invariant. At the other end of the solvent comes the same membrane again. That's what it means to have periodic boundary conditions. The system is good as it is.
Happy simulating!
Boxes have no location. The system is periodic, infinite and translation invariant. At the other end of the solvent comes the same membrane again. That's what it means to have periodic boundary conditions. The system is good as it is.
Happy simulating!
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- xavier
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2 years 6 months ago #9171
by xavier
Replied by xavier on topic Defining box location in INSANE
Hi Peter,
Tsjerk is correct.
What you might want to do is "entering" your system in the box with insane.
The flag -center does it. Then if a side of your bilayer is empty or vacuumed, it does not make sense as the system in infinite by periodic repetition but the central/original system has a finite size, which is repeated.
Good luck
Tsjerk is correct.
What you might want to do is "entering" your system in the box with insane.
The flag -center does it. Then if a side of your bilayer is empty or vacuumed, it does not make sense as the system in infinite by periodic repetition but the central/original system has a finite size, which is repeated.
Good luck
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- peter
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2 years 6 months ago #9185
by peter
Replied by peter on topic Defining box location in INSANE
Hello
Thanks a lot for your replies.
I came across this Martini 3 tutorial . As per the instructions given there, I placed the ligand molecules somewhere within the solvent-ion region.
Hopefully, this would work!
&tsjerk
xavier
Thanks a lot for your replies.
I came across this Martini 3 tutorial . As per the instructions given there, I placed the ligand molecules somewhere within the solvent-ion region.
Hopefully, this would work!
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