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

[Tsjerk Wassenaar]

Hi Stephane,

It's one of the caveats of a reduced resolution model. You loose
detail, like the distinction between decane and dodecane. Although,
there are two bonds and an angle to make a difference.

> 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) ?

You can do anything you like in modeling. It may make sense :) But
different masses on the beads won't give you differences other than
kinetic.

Cheers,

Tsjerk


-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada