[gmx-users] How to differenciate Decane and Dodecane with the Martini force field

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Tue Feb 26 16:41:20 CET 2013

Hello all,

Sorry if it is not the right place to ask the question, but i have a doubt about  the topology for alkanes with MARTINI

Since in Martini
- the default mapping is  4 AA -> 1 bead 
- that in the martini_"v2.0_solvents.itp file" it is stated that the DECANE has the same topology as dodecane mol modeled both with 3 beads (C1 with the same mass).

It is not clear to me how I can differentiate the properties of decane and dodecane. 

Additionally, can i change of the mass of each bead the mass of Decane/3 in the itp file instead of the default mass for C1 (72 AMU) ?

Thank you in advance


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