normal PEGylated Lipid

  • dariush
  • dariush's Avatar Topic Author
  • Offline
  • Senior Boarder
More
4 months 1 week 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

Please Log in or Create an account to join the conversation.

More
4 months 1 week 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

Please Log in or Create an account to join the conversation.

  • dariush
  • dariush's Avatar Topic Author
  • Offline
  • Senior Boarder
More
4 months 1 week 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

Please Log in or Create an account to join the conversation.

  • dariush
  • dariush's Avatar Topic Author
  • Offline
  • Senior Boarder
More
4 months 2 days ago #8002 by dariush
Replied by dariush on topic PEGylated Lipid
Hello,

I'm looking forward to your response.

Best,
Dariush

Please Log in or Create an account to join the conversation.

More
4 months 2 days 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

Please Log in or Create an account to join the conversation.

More
3 months 3 weeks ago - 3 months 3 weeks 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: 3 months 3 weeks ago by bart.

Please Log in or Create an account to join the conversation.

Time to create page: 0.101 seconds