[gmx-users] Micelle Modeling

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 12 17:46:30 CEST 2011

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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