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inconsistent topology in example applications for bilamellar DOPE?
- npokhrel
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5 years 5 months ago #7835
by npokhrel
inconsistent topology in example applications for bilamellar DOPE? was created by npokhrel
Hi Martini World,
I am trying to reproduce a result related to Bi-lamellar DOPE system. The example application section here, provides a gro, mdp and top file. However, I noticed an inconsistency in the number of lipid beads that are used in the *top and the *gro file. It looks like the *gro file was build for a very early version of martini (not exactly sure which one). The reason I say that is because, DOPE has 14 beads instead of 12. Could anyone point me towards a DOPE topology with 14 beads? Or even better, provide me with an updated gro file that is in bilamellar phase?
Here is the link to the Bi-lamellar DOPE system, www.cgmartini.nl/index.php/example-appli...ons2/lipid-membranes .
Thanks!
I am trying to reproduce a result related to Bi-lamellar DOPE system. The example application section here, provides a gro, mdp and top file. However, I noticed an inconsistency in the number of lipid beads that are used in the *top and the *gro file. It looks like the *gro file was build for a very early version of martini (not exactly sure which one). The reason I say that is because, DOPE has 14 beads instead of 12. Could anyone point me towards a DOPE topology with 14 beads? Or even better, provide me with an updated gro file that is in bilamellar phase?
Here is the link to the Bi-lamellar DOPE system, www.cgmartini.nl/index.php/example-appli...ons2/lipid-membranes .
Thanks!
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- bart
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5 years 5 months ago - 5 years 5 months ago #7838
by bart
Replied by bart on topic inconsistent topology in example applications for bilamellar DOPE?
If you want to move on to a working system, I would follow the lipid bilayer tutorial on our webpage. It makes use of insane and allows you to generate most bilayers within a second. I'll take a look at the outdated example you are talking about, but for now the above suggested should get you where you want the quickest.
Last edit: 5 years 5 months ago by bart.
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- riccardo
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5 years 5 months ago #7840
by riccardo
Replied by riccardo on topic inconsistent topology in example applications for bilamellar DOPE?
Not sure about the inconsistency but you can find the latest lipid parameters for a lot of lipids in the lipidome. Here's the page for DOPE:
www.cgmartini.nl/index.php/force-field-p...ml?dir=PE&lipid=DOPE
seems that the 'current' version is the one with 12.
www.cgmartini.nl/index.php/force-field-p...ml?dir=PE&lipid=DOPE
seems that the 'current' version is the one with 12.
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- npokhrel
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5 years 5 months ago #7841
by npokhrel
Replied by npokhrel on topic inconsistent topology in example applications for bilamellar DOPE?
Thanks bart!
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- npokhrel
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5 years 5 months ago #7842
by npokhrel
Replied by npokhrel on topic inconsistent topology in example applications for bilamellar DOPE?
Thanks Riccardo. With the old DOPE, which has 14 beads, I can run the example simulation.
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