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Using insane.py from Martini 2
- hawo
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3 years 4 months ago - 3 years 4 months ago #8794
by hawo
Using insane.py from Martini 2 was created by hawo
Hello everyone.
Is the insane.py script for Martini 2 suitable for use with Martini 3, as long as I just solvate the protein with simple water? I've noticed that the name of the water residue in Martini 3 is different from Martini 2 (WN vs W), are there any other differences that I should be aware of?
Is the insane.py script for Martini 2 suitable for use with Martini 3, as long as I just solvate the protein with simple water? I've noticed that the name of the water residue in Martini 3 is different from Martini 2 (WN vs W), are there any other differences that I should be aware of?
Last edit: 3 years 4 months ago by hawo.
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- riccardo
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3 years 3 months ago #8798
by riccardo
Replied by riccardo on topic Using insane.py from Martini 2
Yes, you can use Insane. When using the Martini 3 open-beta parameters, you should indeed change the name of the water and the name of the ions - please see the "Summary_v3.0.b.3.2.pdf" included in the open-beta parameter package (
cgmartini.nl/index.php/martini3beta
). The relevant section of that pdf is shown below:
"Quick start with MARTINI 3
[...]
- Building your simulation box with a bilayer: As the mapping (and number of beads) of the main lipids did not change from version 2 to 3, you can continue using your favorite programs to build bilayers. We recommend Insane (12) or CHARMM-GUI (13, 14). Only remember to change the name of your water (from W to WN) and ions (from NA and CL to TNA and TCL, respectively) in your top file. PS: new cholesterol and glycolipid models for MARTINI 3 are not available yet.
[...]"
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- z.sichaib
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2 years 10 months ago #8973
by z.sichaib
Replied by z.sichaib on topic Using insane.py from Martini 2
Dear Riccardo,
I am interested in simulating a membrane with CHOL (and other lipids like cardiolipines) using martini v3 however the parameters of these lipids are not available yet.
Can I still use the old itp parameters for cholesterol and cardiolipin with Martini3, while at the same time using the new parameters for other lipids (like POPC and POG?)
Many thanks for the clarifications.
I am interested in simulating a membrane with CHOL (and other lipids like cardiolipines) using martini v3 however the parameters of these lipids are not available yet.
Can I still use the old itp parameters for cholesterol and cardiolipin with Martini3, while at the same time using the new parameters for other lipids (like POPC and POG?)
Many thanks for the clarifications.
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- riccardo
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2 years 10 months ago #8977
by riccardo
Replied by riccardo on topic Using insane.py from Martini 2
No, you can't mix and match martini 2 and 3. See also my answer here:
www.cgmartini.nl/index.php/component/kun...ni2-to-martini3#8965
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