normal DSPC vs DPPC

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10 months 1 week ago #7726 by dariush
DSPC vs DPPC was created by dariush
Hello,

As we all know, the Tm for DSPC and DPPC are ~55 and 41 C, respectively. However, the MARTINI models for these lipids are similar.

Based on this paper:
www.sciencedirect.com/science/article/pii/S0005273616302760

it seems the predicted Tm for DPPC is about right. However still far from Tm for DSPC. Is there a way to play with parameters to make the DSPC model closer to atomistic and experimental values?

Cheers!
Dariush

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10 months 1 week ago #7733 by dariush
Replied by dariush on topic DSPC vs DPPC
Any thoughts/suggestions would be appreciated.

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9 months 3 weeks ago #7765 by dariush
Replied by dariush on topic DSPC vs DPPC
Any thoughts/suggestions would be appreciated.

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9 months 1 week ago #7783 by helgi
Replied by helgi on topic DSPC vs DPPC
Sadly, in Martini both DSPC and DPPC are modeled with the same DPPC lipid (due to the building block strategy they both map to the same number of CG beads).

There is no simple way to fix this. Normal Martini strategy e.g. to see the effect of thicker bilayers would be to use Martini DPPC and DBPC (C20-22:0) and look at the trend.

If you really need a more actuate Martini model of DSPC you can try to adapt the current DPPC model by e.g. extending the bond lengths between the carbon beads but this should be done with grate care and with respect to reference atomistic simulations.

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