[gmx-users] Micelle Modeling

[Justin A. Lemkul]

Janowicz, Adrianna C. wrote:
> Users,
> I'm trying to start a micelle modeling project & have tried countless
> approaches to making a DPC micelle. My problems include:
> -DPC not being recognized when I try to imput it into the [molecules]
> seciton of the topology file to account for the DPC molecules in the water
> topology. Otherwise, the molecule #s do not match. (This approach included
> using a coordinate file for DPC & using the -nmol fuction in genbox to
> place the DPC molecules into the water).
> 
> I would appreciate any help. Even if this means taking a totally different
> approach in getting the DPC molecules into the box.
> 

The best approach would be to:

1. Create the topology for a single molecule of DPC
2. Generate a configuration of the DPC micelle and edit the number of molecules 
in the .top appropriately
3. Solvate and let genbox add the correct number of water molecules to the .top

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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