normal How to rotate the system

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11 years 9 months ago #1032 by richor
How to rotate the system was created by richor
Dear Martini users:

After running the dspc for 27ns,I find the bilayer isn't in the x-y plane.
Then I use the editconf to rotate it,but how can I know the rotating angle ?

Does anyone can answer me?

Very appreciate for your reply!

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11 years 9 months ago #1033 by djurre
Replied by djurre on topic How to rotate the system
As far as I can see the bilayer can be in any of the planes (xy, yz, xz) or along a diagonal. In the first case you need to rotate it 90degrees around the 'non-Z-axis (eg: yz > xy = 0 90 0). In the second case, if the diagonal is: in yz plane, rotate by (45 0 0), in the xz plane, rotate by (0 45 0) and in the xy plane, rotate by (90 0 45) or (0 90 45).

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11 years 9 months ago #1034 by richor
Replied by richor on topic How to rotate the system
Dear djurre:
Thank you for your reply!
Actually the bilayer is along a diagonal,but not accurate.
I rotate it by (-30 0 0),and then make the system bigger to contain all the
moleculars.
Did I do this right? How do you handle this when you come across it?
Appriciate for your reply!

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11 years 9 months ago #1035 by djurre
Replied by djurre on topic How to rotate the system
I think I always redid the simulation with different starting velocities. It's so fast, why not... If you actually want to use the bilayer (as in: not only do it for the tutorial) you can also use the preformed bilayer at the website.

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11 years 9 months ago #1037 by richor
Replied by richor on topic How to rotate the system
Dear djurre:
Thanks for your suggestion.
Actually I want to run for a different lipid molecular.
Thankfully, I gained the bilayer after running for several times.
Then I have another question.
It seems that I need to run many times to gain the bilayer right in any of the planes (xy, yz, xz) as the probability of any direction is 1/4pi.
However,the fourth is perfect. I don't think it's just lucky. Is there anything affect this? What's your opinion?
Appriciate for your reply!

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11 years 9 months ago #1041 by syahidah
Replied by syahidah on topic How to rotate the system
Hi Richor,

i am also new with CGMD and Martini=),

from my experince doing the tutorial,
the energy minimization stage is very important in order to get the bilayer,
meaning during the energy minimization (before and after adding the water), we need to make sure that the energy is converged..otherwise, the bilayer could not form..

this is my 20cents only since i'm still new in this field..

best,
syahida

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