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Lipid14 simulations #7

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jmelcr opened this issue Sep 17, 2016 · 8 comments

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@jmelcr
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commented Sep 17, 2016

Hi, is someone running simulations for Lipid14?
There are parameters for cholesterol and the authors themselves made simulations with various cholesterol content - has anyone already asked them to share?

@ohsOllila

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commented Sep 17, 2016

I am going to contact them. They report order parameters in the publication and even compare to the same NMR dataset we are using. Those we could take directly from figures but I hope that they could give us, at least, numerical results for those. Form factors would be nice as well. Also if someone else has Lipid14 simulations with cholesterol, let us know.

@MykhailoGirych

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commented Sep 17, 2016

Hi, I'm going to convert Lipid14 parameters for cholesterol into Gromacs format and start the simulations in Sep. I will share the data as soon as I get it.

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commented Sep 19, 2016

Good! I wanted to know whether there's something going on or whether we need to simulate it ourselves (which might still be fine to do for a check).

@MykhailoGirych
Could you share the parameters (files) with us even before the simulations are done, please?

@jjmadsen

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commented May 10, 2019

I have experimented with running lipid14 in amber before and can run some dynamics trajectories that are needed.

@MykhailoGirych
How far did you get and which concentrations of interest are still missing?

@MykhailoGirych

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commented May 10, 2019

@jjmadsen The simulations in lipid14 are running (with the updated partial charges for POPC and CHOL taken from Lipid17). @jmelcr I'll share the parameters I use in a few days.

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commented May 13, 2019

@MykhailoGirych Great..Which concentrations are you running currently? I'd be happy to help out with this.

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commented Jun 3, 2019

@MykhailoGirych Hi, How's it going on this?

@ohsOllila

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commented Jun 14, 2019

@MykhailoGirych informed in Skype that he has the data, but he has not had time to upload it into Zenodo yet.

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