normal PEGylated Lipid

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5 years 2 months ago #7985 by dariush
PEGylated Lipid was created by dariush
Hello,

I recently started working with PEGYLATED LIPIDs.
I learned there is a huge fore constant at the point lipid is attached to polymer, which makes my simulations very unstable. I played a little bit with this value which was originally set to 17000. When I reduce it to less than 10000 the issue was fixed.
I'd like to know the chemistry reasoning behind picking this value? While I don't think this change may affect significantly the results of my qualitative simulations, I'd like to know how much I am allowed to modify this specific parameter.

Thanks!
Dariush

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5 years 2 months ago #7987 by bart
Replied by bart on topic PEGylated Lipid
Heya,

Could you maybe link the file you used for the PEGYLATED LIPIDS? I looked on our website and I couldn't find any PEGYLATED LIPID with a high force constant in its connecting bonds. Maybe a link to your file or just copy the important part yourself with a description how you got it.

Cheers,

Bart

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5 years 2 months ago #7997 by dariush
Replied by dariush on topic PEGylated Lipid
Hi Bart,

Could you please look at these two links from the website:
PEGylated DOPE:
cgmartini.nl/images/parameters/polymers/...tini_v2.0_PEL_45.itp

and PEL from this file:
cgmartini.nl/images/parameters/ITP/martini_v2.0_polymers.itp

There is a discrepancy in these files. In the first, the force constant is 7000 and in the second one 17000. Unfortunately, I had started with the second set of parameters, and I just found out the first file, in which force constants make much more sense to me (lower values).

Thank you for answering!
Dariush

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5 years 2 months ago #8002 by dariush
Replied by dariush on topic PEGylated Lipid
Hello,

I'm looking forward to your response.

Best,
Dariush

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5 years 2 months ago #8003 by riccardo
Replied by riccardo on topic PEGylated Lipid
Hi Dariush,

I don't know precisely about the discrepancy in the force constants (did you check whether the respective publications -- F. Grunewald, et al 10.1021/acs.jpcb.8b04760 and Lee & Pastor, J. Phys. Chem. B, 2011, 115, 7830-7837 + Lee, de Vries, Marrink, Pastor, J. Phys. Chem. B, 2009, 113, 13186-13194 -- mention/show plots to justify their values?), but I would recommend using the latest parameters, so:

cgmartini.nl/images/parameters/polymers/...tini_v2.0_PEL_45.itp

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5 years 1 month ago - 5 years 1 month ago #8029 by bart
Replied by bart on topic PEGylated Lipid
Sorry for the late reply, I was quite busy lately. But yes, like Riccardo said, I would take a look at the original paper and use what they used. If of is unclear I would go for the latest one, or even better, do some test en check for yourself.
Last edit: 5 years 1 month ago by bart.

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