normal EM of DNA origami

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3 years 10 months ago #8524 by Fondyffendof
EM of DNA origami was created by Fondyffendof
Hi all
So i am running into some trouble with my structure during energy minimization.
I don't know what is happening i have tried reaction-field/PME, changing the time step, cut off ranges, adding up to 20000 Na and Cl ions, having an emstep=0.01, but after 10-40 steps LINCS warnings arrive on some of the atoms in the bases.
using trjconv shows blow off of bases and sticking together in clumps or the strands jump over each other.
Any idea of what i could change, the initial structure looks as it should.
I used an equlibrated water box to solvate the system, and only modified to topology file for ions and WF as was done in DNA tutorial.

Thanks for any advice's :)

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3 years 10 months ago #8525 by Fondyffendof
Replied by Fondyffendof on topic EM of DNA origami
further notes:
I am using PBC=xyz, could this cause trouble with multiple strands when one strands leaves at the end?

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3 years 10 months ago #8556 by vainikka
Replied by vainikka on topic EM of DNA origami
Hi,

A few questions:
You say your starting structure looks as it should, but assuming from the number of (counter)ions you've added, it's a pretty large system. Are you sure there are no clashing or overlapping atoms?

How did you obtain the parameters for this system? If your system contains multiple components, have you tried minimizing them separately?

Your current PB conditions shouldn't be the issue.

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3 years 10 months ago #8565 by Fondyffendof
Replied by Fondyffendof on topic EM of DNA origami
I found the problem with the way the martinize-dna script reads the DNA.

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3 years 10 months ago #8567 by vainikka
Replied by vainikka on topic EM of DNA origami
Good to hear! Could you post a quick explanation here, so that we can refer to it in the future?

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3 years 10 months ago #8570 by Fondyffendof
Replied by Fondyffendof on topic EM of DNA origami
I think it was just a misunderstanding from my part that the dsdna model reads a strand and splits it in two single strands connected.

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3 years 10 months ago #8571 by Fondyffendof
Replied by Fondyffendof on topic EM of DNA origami
I think it was just a misunderstanding from my part that the dsdna model reads a strand and splits it in two single strands connected.
Using ssdna it worked

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